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

The prevalence of antibodies against the HLA-DRB3 protein in kidney transplantation and the correlation with HLA expression

Human leukocyte antigen (HLA)-DRB3 is a functional HLA class II gene, which has a limited allele diversity in the human population. Furthermore, the HLA-DRB3 gene is only present in a subset of individuals. Therefore, in organ transplantation, this HLA molecule is frequently mismatched between patient and graft donor and thus antibodies against this mismatched HLA molecule can develop. In this study, we aimed to evaluate the prevalence and reactivity of these antibodies and aimed to identify factors that underlie antibody formation against HLA-DRB3. We showed in our patient cohort that HLA-DRB3 antibodies are identified in about 7% of all patients that were screened with solid phase assays. In these assays, we observed multiple antibody reactivity patterns indicating that HLA-DRB3 harbours multiple epitopes. In those cases, where we succeeded at tracing back the induction of these antibodies to the molecular HLA typing of the immunogenic event, we noticed a different frequency of HLA-DRB1 allele groups in the donors as compared to a control group. To a certain extent this distribution (e.g. HLA-DRB1*11 individuals) could be linked to an altered expression level. However, it also appears that different HLA-DRB3 alleles (e.g. HLA-DRB3*01 group) vary in their immunogenicity without having an expression difference. In conclusion, our study provides information on the immunogenicity and reactivity patterns of antibodies against HLA-DRB3 in kidney transplantation, and it points towards the possibility of HLA expression as a factor underlying antibody formation.

HLA class-I and HLA class-II phenotypic, gene and haplotypic frequencies in Tunisians by using molecular typing data

The aim of this study is to define a reliable reckoning of gene frequencies and six-locus haplotypic frequencies of HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1 and HLA-DPB1 in the Tunisian population. One hundred unrelated random, healthy people originating from various parts of Tunisia were typed for the alleles of the loci mentioned above by using the molecular techniques polymerase chain reaction--hybridization with oligonucleotide probe (PCR-SSO) and sequence specific primers (SSP). The population studied appeared to be in Hardy-Weinberg equilibrium. Allelic frequency distributions were observed at each locus. The most frequent HLA-A alleles were HLA-A*02 (39%) HLA-A*0101 (25%), HLA-A*30 (21%) and HLA-A*2301 (18%). Moreover, HLA-3A*3601, HLA-1A*6601, HLA-1A*3402 and HLA-2A*8001 were found; however, no HLA-A*4301 was detected. For the HLA-B locus, the most common in descending order were HLA-B*44 (22%), HLA-B*5001 (19%), HLA-B*51 (16%) and HLA-B*18 (15%). Among the 28 alleles HLA-Cw detected, HLA-Cw*6 and HLA-Cw*7 were highly predominant with the frequencies of 33 and 30%, respectively. For the HLA class-II loci, HLA-DRB1*0701, HLA-DRB1*11, HLA-DRB1*13 and HLA-DRB1*03 were the most frequent DR alleles. For the HLA-DPB1, HLA-DPB1*0401, HLA-DPB1*0301 and HLA-DPB1*0201 were the most frequent DP alleles. Many haplotypes were in a strong positive-linkage disequilibrium. The most frequent haplotypes for HLA-A, HLA-B, HLA-C and HLA-DRDQ were HLA-A*3301, HLA-B*1402, HLA-Cw*0802, HLA-DRB1*0102, HLA-DQA1*0101 and HLA-DQB1*0501; HLA-A*2402, HLA-B*0801, HLA-Cw*0702, HLA-DRB1*0301, HLA-DQA1*0501 and HLA-DQB1*0201; HLA-A*2902, HLA-B*4403.1, HLA-Cw*1601, HLA-DRB1*0701, HLA-DQA1*0201 and HLA-DQB1*0202; HLA-A*3002, HLA-B*1801, HLA-Cw*0501, HLA-DRB1*0301, HLA-DQA1*0501 and HLA-DQB1*0201, with frequencies between 0.025 and 0.015. These data can be used as control data for HLA disease associations and paternity studies, but they are also important for the evaluation of the probability rate of success in determining the optimal matched donor in unrelated stem transplantation for Tunisian patients or patients of Tunisian origin.

Processing of the DRB1*1103-restricted measles virus nucleoprotein determinant 185-199 in the endosomal compartment

MHC class II molecules present to CD4+ T cells protein fragments which mostly derive from the extracellular and from the endosomal compartments. Determinants of cytosolic proteins are, however, also displayed by MHC class II molecules following pathways which are still not yet fully characterized. Here we describe the isolation of DRB1*1103-restricted T cell clones specific for the measles virus (MV) nucleoprotein peptide 185-199 (N185). Experiments were then conducted to delineate how this determinant is assembled with DR molecules. In vitro binding analyses indicated that complexes between the N185 peptide and DRB1*1103 protein are optimally constituted at pH 4-4.5. In cellular experiments it was observed that chloroquine, leupeptin and emetine, which are classical inhibitors of presentation of MHC class II-restricted antigens, when added during infection of B cells with MV, prevent presentation of the N185 determinant. In addition, it was found that the N185 determinant is efficiently presented when the nucleoprotein is exogenously provided to B cells, either by blocking MV fusion with the peptide FFG or by the use of purified nucleoprotein. In contrast, it was observed that nucleoprotein recombinant vaccinia virus (vv-N)-infected B cells weakly stimulated N185-specific T cells, indicating that the restricted localization of the nucleoprotein in the cytosol resulted in a poor presentation of the N185 determinant. Taken together, these findings suggest that it is prior to delivery of the nucleoprotein into the cytosol that the N185 determinant is efficiently assembled with newly synthesized DR molecules in the acidic environment of the endosomal compartment.

Determination of DQB1 alleles using PCR amplification and allele-specific primers

Molecular genotyping of HLA class II genes is commonly carried out using polymerase chain reaction (PCR) in combination with sequence-specific oligotyping (PCR-SSO) or a combination of the PCR and restriction fragment length polymorphism methods (PCR-RFLP). However, the identification of the DQB1 type by PCR-SSO and PCR-RFLP is very time-consuming which is disadvantageous for the typing of cadaveric organ donors. We have developed a DQB1 typing method using PCR in combination with allele-specific amplification (PCR-ASA), which allows the identification of the 17 most frequent alleles in one step using seven amplification mixtures. PCR allele-specific amplification HLA-DQB1 typing is easy to perform, and the results are easy to interpret in routine clinical practice. The PCR-ASA method is therefore better suited to DQB1 typing for organ transplantation than other methods.

Population diversity of B-locus alleles observed by high-resolution DNA typing

HLA B-locus typing by group-specific PCR and hybridization with SSOP was performed in 81 10th IHWS B cell lines and 334 selected subjects of our local panel, from four ethnic groups. Most of the B-locus serological specificities were well defined. However, some antigens like B41, B58, B56, the splits of B14, and some subtypes of B5, were not accurately assigned by serology. In the panel studied, we found 17 hybridization patterns that corresponded to probable new alleles. New patterns occurred in the four ethnic groups examined. Multiple subtypes of B35, B5, B15, B41, B44, B57, B58, B70, B14, B40, B22 were found in subjects of the same ethnic group. In view of the poor serological definition of some alleles, and the occurrence of multiple subtypes in the same ethnic population, it appears that high resolution B-locus typing may be an important addition for detection of potentially relevant HLA incompatibilities in transplantation. It should also be valuable for population studies and for the investigation of HLA associations with diseases.

High resolution HLA-DRB1 SSP typing for cadaveric donor transplantation

An HLA-DRB1 typing procedure by means of sequence-specific primer (SSP) amplification was developed for 65 different DRB1 subtypes. Subtyping is achieved by the performance of two subsequent PCR assays (PCR-1 assay and PCR-2 assay) using a limited number of reactions. The PCR-1 assay determined low-resolution HLA-DRB1 typing, i.e. the serologically defined specificities DR1, 2, 3, 4, 11, 12, 6, 7, 8, 9 and 10. The second exon of the DRB1 gene is amplified also in this PCR-1 assay. High-resolution subtyping for positively identified alleles was performed in the PCR-2 assay with the exon-2 product from PCR-1 assay as DNA template. PCR reactions were carried out using unpurified primers in reaction volumes of 20 microliters and 100 ng of chromosomal DNA. After 3 hours, the results of the PCR-1 assay were analyzed and subsequently subtyping results in the PCR-2 assay were obtained in another 1.5 hours. A total of 249 DNA samples was typed by this method. No false positive nor false negative results were obtained in DRB1 typing of 32 homozygous cell lines, 56 serologically well-defined panel cells and 125 unrelated individuals. Segregation of the amplification patterns was investigated in 36 members of 7 two-generation families. DRB1 subtyping revealed codominant Mendelian segregation for all subtypes investigated. In conclusion, LR-HR-PCR-SSP typing is a fast and reliable typing technique for routine DNA typing purposes which gives complete DRB1 subtyping within 4.5 h. Besides low-resolution DRB typing, also high-resolution DRB subtyping for prospective HLA-DR matching in cadaveric renal transplantation is possible by this method.

Human CD4+ T cells specifically recognize a shared melanoma-associated antigen encoded by the tyrosinase gene

Although commonly expressed human melanoma-associated antigens recognized by CD8+ cytolytic T cells have been described, little is known about CD4+ T-cell recognition of melanoma-associated antigens. Epstein-Barr virus-transformed B cells were used to present antigens derived from whole cell lysates of autologous and allogeneic melanomas for recognition by melanoma-specific CD4+ T-cell lines and clones cultured from tumor-infiltrating lymphocytes. HLA-DR-restricted antigens were detected in the lysates on the basis of specific release of cytokines from the responding T cells. Antigen sharing was demonstrated in the majority of melanomas tested, as well as in cultured normal melanocytes, but not in other normal tissues or nonmelanoma tumors. T-cell clones manifested a single recognition pattern, suggesting the presence of an immunodominant epitope. This epitope was identified as a product of the tyrosinase gene, which has also been shown to encode class I-restricted epitopes recognized by CD8+ T cells from melanoma patients. Identification of commonly expressed tumor-associated protein molecules containing epitopes presented by both class I and class II major histocompatibility molecules may provide optimal reagents for cancer immunization strategies.

Determination of DRB alleles using PCR amplification and allele-specific primers

HLA class-II allelic diversity is commonly defined using polymerase chain reaction (PCR) in combination with sequence-specific oligotyping (PCR-SSO) or the combination of PCR and restriction fragment length polymorphism methods (PCR-RFLP). Nevertheless, the identification of the DRB polymorphism by PCR-SSO is a time-consuming procedure and the PCR-RFLP is cumbersome. A rapid technique which allows a precise and extensive HLA-DRB typing is required, particularly in order to study the role of class-II matching in organ transplantation. A DRB typing method based on the detection and length of PCR products amplified using combination of allele specific primers has been developed. Thirty-four DRB alleles (29 DRB1, 4DRB3, 1DRB4) can be detected using 29 primers distributed into 19 amplification mixtures.

Functional dissection of the serological DR LYGUE and genotypic DRB1*1303 specificities using a tetanus toxin-specific T-cell clone

The DRB1 sequence of the homozygous cell line HAG (DR13-DwHAG-DQ7) represents a new DRB allele assigned DRB1*1103, whereas its DRB3 sequence corresponds to the previously described DRB3*0101 (DR52a) allele. The DRB1*1303 gene product is undetectable by current sera used in routine serology typing. We report here direct evidence that the MHC molecule encoded by the DRB1*1303 gene is functional in antigen presentation and in T-cell restriction. We describe a T-cell clone specific for tetanus toxin whose restriction pattern strictly follows the DRB1*1303 allele, as defined by oligonucleotide typing. It also follows the serologic reactivity with the serum LYGUE and also the DwHAG MLC-defined specificity pattern, with one exception. The potential functional sites for the DRB1*1303 gene product involved in T-cell restriction were deduced from sequence comparisons between DRB1*1303 and closely related DRB1 alleles. The relevant as substitutions were located within close proximity to each other on the HLA class II structural model. Our results demonstrate that 1) DRB1*1303 is functional in antigen presentation and T-cell restriction 2) the functional region involved in antigen presentation and T-cell restriction by DRB1*1303 can be defined structurally.

Oligonucleotide genotyping of HLA polymorphism on microtitre plates

Molecular analysis of mutations and polymorphisms that are of medical importance requires both accuracy and simplicity. In organ transplantation there is a need for an HLA typing procedure that combines the remarkable accuracy of oligonucleotide genotyping with the simplicity of conventional serological typing. We describe a simple semiautomated method of HLA class II typing consisting of an oligonucleotide hybridisation assay done on microtitre plates followed by automatic colorimetric reading. Individual HLA-DR generic typing for 30 DR specificities, including subtypes of DR1, DR2, DR13, DR14, and DR52, is done on a single plate. The entire typing assay can be completed in less than 4 hours. The procedure has been validated on more than a thousand haplotypes in prospective DR typing of kidney transplant patients, leukaemic patients, and their potential donors. The simplicity of this assay makes it suitable for routine laboratory use. It can be applied to genetic testing in general, including the testing of patients with multiple mutations.

Serological and molecular analysis of HLA in Israeli primary sclerosing cholangitis patients

HLA class I and class II were investigated in 15 Israeli primary sclerosing cholangitis patients and compared to healthy controls. None of the well established serological specificities were found to be associated with the disease. HLA-DR52 is serologically defined, but its subtypes DR52a, DR52b, and DR52c cannot be precisely defined by serological means. Therefore, we have used HLA-DNA typing in order to assign the DR52 splits in PSC patients. Genomic DNA was amplified by PCR, dot-blotted and hybridized with sequence specific oligonucleotide probes defining the known HLA-DR52 associated alleles. Only 4 out of the 15 PSC patients tested were found to express DRB3*0101 the allele that encodes DR52a. Of the remaining 11 patients, 9 expressed DRB3*0202 haplotypes, with 2 patients expressing both DRB3*0101 and DRB3*0202, and the remaining 2 patients expressed no DRB3 allele. Our data indicate that there is no apparent association between PSC and the HLA antigens and alleles studied including the alleles of the DRB3 locus in the Israeli population. Thus HLA pheno/genotyping of PSC patients in the Israelis will not be useful for early and/or differential diagnosis of this disease.

HLA-DR polymorphism in a Senegalese Mandenka population: DNA oligotyping and population genetics of DRB1 specificities

HLA class II loci are useful markers in human population genetics, because they are extremely variable and because new molecular techniques allow large-scale analysis of DNA allele frequencies. Direct DNA typing by hybridization with sequence-specific oligonucleotide probes (HLA oligotyping) after enzymatic in vitro PCR amplification detects HLA allelic polymorphisms for all class II loci. A detailed HLA-DR oligotyping analysis of 191 individuals from a geographically, culturally, and genetically well-defined western African population, the Mandenkalu, reveals a high degree of polymorphism, with at least 24 alleles and a heterozygosity level of .884 for the DRB1 locus. The allele DRB1*1304, defined by DNA sequencing of the DRB1 first-domain exon, is the most frequent allele (27.1%). It accounts for an unusually high DR13 frequency, which is nevertheless within the neutral frequency range. The next most frequent specificities are DR11, DR3, and DR8. Among DRB3-encoded alleles, DR52b (DRB3*02) represents as much as 80.7% of all DR52 haplotypes. A survey of HLA-DR specificities in populations from different continents shows a significant positive correlation between genetic and geographic differentiation patterns. A homozygosity test for selective neutrality of DR specificities is not significant for the Mandenka population but is rejected for 20 of 24 populations. Observed high heterozygosity levels in tested populations are compatible with an overdominant model with a small selective advantage for heterozygotes.

HLA class II genes in primary sclerosing cholangitis and chronic inflammatory bowel disease: no HLA-DRw52a association in Swedish patients with sclerosing cholangitis

The familial predisposition to chronic inflammatory bowel disease and the increased concordance rate in monozygotic twins with Crohn's disease, suggest that genetic factors influence disease susceptibility. A 100% association with the supertypic HLA class II specificity DRw52a was recently described in white North American patients with primary sclerosing cholangitis, with or without concurrent ulcerative colitis. HLA class II alleles of the DR, DQ, and DP subregions were determined by genomic typing techniques in a large group of Swedish patients with ulcerative colitis or Crohn's disease as well as in a series of patients with primary sclerosing cholangitis. No statistically significant HLA class II association was observed in any of the investigated diseases or when the patients were subgrouped according to disease site or occurrence of extraintestinal manifestations, except an insignificant increase of the DRw17, DQw2 haplotype in patients with primary sclerosing cholangitis. The failure to confirm the well established DRw17 association in Swedish patients with sclerosing cholangitis probably represents a statistical type II error. Furthermore, this study did not verify the recently described strong DRw52a association in sclerosing cholangitis--52% of the patients were DRw52a positive compared with 28% of the controls (p less than 0.05, pc NS). This discrepancy was probably caused by different typing techniques. The DRw52a specificity was determined directly by hybridising HLA-DRB3 genes, group specifically amplified by the polymerase chain reaction, with an allele specific oligonucleotide probe, whereas in the previously mentioned study DRw52a was assigned by indirect serological criteria, which overestimate the frequency of this allele.

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.

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.

Studies of the HLA class II alleles involved in human responses to ragweed allergensAmbrosia artemisiifoliaV (Ra5S) andAmbrosia trifidaV (Ra5G)

Previous studies have associated skin test sensitivity and specific IgE response to Ambrosia artemisiifolia V (Amb a V) with HLA-DR2, and to Ambrosia trifida V (Amb t V) with HLA-DRw52 haplotypes in atopic individuals. Using HLA class II typing by restriction fragment length polymorphism (RFLP) analysis with DRB, DQB and DQA DNA probes to define the HLA-D alleles, we have demonstrated the association of the DQw6 in 16 out of 16 (100%) Amb a V-responsive individuals, compared to 3 out of 18 (17%) ragweed-sensitive but Amb a V-nonresponsive individuals (p = 5.7 x 10(-6), RR greater than 75). We suggest that the DQw6 association with Amb a V sensitivity may be a reflection of an association with the DQA*0102 allele. This suggests an association of a particular HLA class II allele with an immune response to a well-characterized antigen (Amb a V). The HLA-DRw52 haplotypes in the Amb t V-sensitive individuals are not of one particular subtype. The HLA-DRw52 association with Amb t V sensitivity may reside in homologous DRB1 alleles linked on HLA-DRw52-bearing haplotypes.

HLA-DR gene frequencies in the Japanese population obtained by oligonucleotide genotyping

We determined HLA-DRB types of 375 randomly chosen healthy Japanese donors using a set of 29 different sequence-specific oligonucleotide (SSO) probes directed against various DRB alleles. Except for a few cases, these SSOs enabled us to identify 33 different DRB types including those detectable only by SSO genotyping. Gene frequencies were calculated for each of the DRB types identified. The "blank" frequency calculated by our SSO typing was essentially zero, in contrast to the considerably high "blank" frequencies reported at serological HLA-DR or cellular HLA-D workshops. This indicates that almost all of the DRB types in the Japanese population are positively detectable by our SSO typing. By comparing the gene frequencies for each of the DR types obtained by our SSO typing with those obtained by immunological typing at workshops, significant differences were observed for several of the DR types.

Selection of unrelated donors for bone marrow transplantation is improved by HLA class II genotyping with oligonucleotide hybridization

As the demand for donors for bone marrow transplantation increases, the use of HLA-matched, genetically unrelated donors represents a promising strategy. It is well documented that the clinical outcome of bone marrow transplantation is directly dependent on optimal matching for HLA class I and class II specificities. Molecular studies have revealed the existence of a much larger number of HLA class II alleles than was anticipated, many of which cannot be recognized by routine serological typing. Currently this "hidden" polymorphism represents a major limitation to the generalized use of unrelated donors for bone marrow transplantation. It has recently become possible, however, to identify HLA allelic polymorphism directly at the DNA level by hybridization with sequence-specific oligonucleotide probes ("HLA oligotyping") after amplification of DNA by polymerase chain reaction. In this study, we have investigated whether donor-recipient pairs that are fully matched for HLA by serology are truly HLA-DR, -DQ, and -DP identical and to what extent class II differences influence the primary mixed lymphocyte culture. We show that HLA oligotyping, performed on 50 pairs of HLA class I and II serologically matched individuals, can indeed reveal phenotypically relevant allelic differences at either DRB or DQB loci in 56% of these pairs and can therefore improve HLA class II typing and the choice of bone marrow donors quite significantly. Oligotyping for DRB/DQB/DPB polymorphism also allows prediction of a positive mixed lymphocyte culture, as established in 31 donor/recipient combinations, and even detection of polymorphic differences that were not revealed by this test. This approach is well suited for accurate HLA typing of large pools of bone marrow donors and was successfully applied to select fully matched donors for bone marrow transplantation.

Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA

Thirty mapped Indica rice genomic (RG) clones were partially sequenced from each end. From such sequence data, pairs of oligonucleotides were synthesized to act as primers for polymerase chain reaction (PCR) amplification of the corresponding loci in crude total DNA preparations. The PCR products from DNA of Indica varieties were of the sizes expected from the sizes of the corresponding RG clones. However, size polymorphisms were seen between PCR products from Indica and Japonica varieties, and among wildOryza species. Restriction fragment length polymorphism (RFLP) was observed between PCR products of Indica varieties simply by electrophoretic analysis of restricted products, without the need for Southern hybridization or radiolabelling. The RFLPs noted between varieties ARC6650 and Phalguna were inherited in recombinant inbred lines derived from a cross between them. The RFLPs were detectable in PCR products amplified from DNA extracted by a simple procedure from single seedlings or leaves, and revealed genetic heterogeneity in cultivated lines. An approach is described that is relevant to the acceleration of classical plant breeding through molecular techniques.

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.

Detection of novel sequence heterogeneity and haplotypic diversity of HLA class II genes

Nucleic acid sequences of the second exons of HLA-DRB1, -DRB3/4/5, -DQB1, and -DQA1 genes were determined from 43 homozygous cell lines, representing each of the known class II haplotypes, and from 30 unrelated Caucasian subjects, comprising 60 haplotypes. This systematic sequence analysis was undertaken in order to a) determine the existence of sequence microheterogeneity among cell lines which type as identical by methods other than sequencing; b) determine whether direct sequencing of class II genes will identify the presence of more extensive sequence polymorphism at the population level than that identified with other typing methods; c) accurately determine the molecular composition of the known class II haplotypes; and d) study their evolutionary relatedness by maximum parsimony analysis. The identification of seven previously unidentified haplotypes carrying five new allelic amino acid sequences suggests that sequence microheterogeneity at the population level may be more frequent than previously thought. Maximum parsimony analysis of these haplotypes allowed their evolutionary classification and indicates that the higher mutation rate at DRB1 compared to DQB1 loci in most haplotypic groups is inversed in specific haplotype lineages. Furthermore, the extent and localization of gene conversions and point mutations at class II loci in the evolution of these haplotypes is significantly different at each locus. Identification of additional HLA class II molecular microheterogeneity suggests that direct sequence analysis of class II HLA genes can uncover new allelic sequences in the population and may represent a useful alternative to current typing methodologies to study the effects of sequence allelism in organ transplantation.

Molecular analysis of HLA DR4-beta 1 gene in malaria vaccinees. Typing and subtyping by PCR technique and oligonucleotides

The combination of the PCR technique and the synthetic oligonucleotides has proved to be a useful tool in the molecular analysis of HLA class II genes, allowing recognition of as little as a single nucleotide modification in the sequence of the gene. The molecules encoded by these genes have been associated with genetic control of the immune response and with susceptibility to certain diseases. Studies carried out in our laboratory have shown three patterns of humoral immune response in the human volunteers vaccinated with the synthetic protein SPf 66; high, intermediate and low responders. Approximately 73.3% of the low responders were serologically typed as HLA DR4 and 42% as DQw6. These results moved us to look for a subtype (Dw) correlation between the DR4 positive individuals and the different humoral immune response patterns. Using oligo-typing methods after previous amplification of the DR4 B1 exon, we subtyped 20 DR4 volunteers, classified as high, intermediate and low responders. We did not find any direct association between the HLA DR4 Dw special subtype in the high or low responders immunized with the SPf 66 vaccine.

The immune response to the HPA-1a antigen: association with HLA-DRw52a

Antibodies to the HPA-1a antigen can elicit a condition in the new-born known as neonatal alloimmune thrombocytopenia (NAITP). Retrospective and prospective studies have shown that there is a strong correlation between the presence of HLA-DR3, HLA-DRw52 in the mother and the antibody response to HPA-1a. HLA Class II molecules play an important role in the initiation of the immune response and it has been postulated that HPA-1a antibody production could be determined by the presence of a specific HLA Class II molecule at the surface of the antigen-presenting cell. Thirty-one HPA-1a negative women with HPA-1a antibodies (responders) and nine HPA-1a negative women without HPA-1a antibodies (non-responders) were recruited. They were studied using serological HLA Class I and Class II typing and RFLP analysis with a DR beta probe. We found that all responders had the HLA-DRw52a sub-specificity confirming recently published data. Moreover, two of the nine non-responders were also found to be HLA-DRw52a. These results suggest that the HLA-DRw52a molecule is necessary for HPA-1a antibody responsiveness but not sufficient. The results also indicate that in HPA-1a negative women the absence of HLA-DRw52a is associated with a very low risk of being antibody producers and hence, is associated with a very low risk for NAITP in their new-borns.

The Eurotransplant HLA-DRB oligonucleotide typing set

Several sequence-specific oligonucleotides (SSO) were designed based upon available sequences of HLA-DRB1 genes which are associated with HLA-DR serotypes. Targets for these SSO were polymerase chain reaction (PCR) products using primers specific for the second exon of DRB genes. In view of practically, a hybridization system was developed which was independent of temperature or composition of the hybridization buffers, hence uniformly applicable to all SSO, yet allowing discrimination based upon one nucleotide mismatch only. The SSO typing results were compared with HLA serological typing and a high correlation was observed (99%).

Combined use of RFLP and PCR-ASO typing for HLA-DR-Dw and DQw typing

Due to some limitations of restriction fragment length polymorphism (RFLP) analysis in HLA-DR-DQ typing, we present a combined use of RFLP and polymerase chain reaction (PCR)-allele-specific oligonucleotide (ASO) typing. This scheme consists in selectively amplifying the few RFLP ill-defined genes (DR1/DR'Br' and DR4-Dw subsets) using PCR with allele specific primers to avoid cross-hybridization.

Absence of DRw15/3 and of DRw15/7 heterozygotes in Caucasian patients with systemic lupus erythematosus

Polymorphic MHC class II molecules determine immune responsiveness towards pathogens and also contribute to susceptibility or resistance to a number of different autoimmune diseases, including systemic lupus erythematosus (SLE). The HLA-DR and -DQ alleles of 52 patients with SLE were analyzed by serology and, for 42 patients, HLA-DRB1, -B3 and DQB1 allelic polymorphism was determined by oligotyping on PCR-amplified DNA. While we confirm the increase of DR3 (44.2% versus 16% in controls; p less than 0.001) reported by others, we observed a complete absence of DRw15(2)/DR3 and DRw15(2)/DR7 heterozygotes among Caucasian patients. Moreover HLA-DQB1 oligotyping revealed the absence of DQB1*0602/0201 heterozygotes in our panel of Caucasoid SLE patients. Since both DR3 and DR7 haplotypes share the same DQB1*0201-encoded DQ beta chain, and since DRw15 is known to be in linkage disequilibrium with DQA1*0102, it can be predicted that DQA1*0102/DQB1*0201 combinations are absent in Caucasian patients. We therefore propose that a DQA1*0201/DQB1*0201-encoded HLA-DQ trans-dimer formed in these heterozygotes might function as a suppressor-inducer molecule that confers resistance against SLE.

HLA antigens in juvenile arthritis. Pauciarticular and polyarticular juvenile arthritis are immunogenetically distinct

Using DNA techniques, we investigated the role of HLA-DR, DQ, and DP alleles in susceptibility to juvenile arthritis (JA). We studied 2 groups of patients with JA having a different disease prognosis and course. The pauciarticular form is usually benign, while the polyarticular disease frequently leads to joint destruction and disability. Persistent pauciarticular disease developed preferentially in patients having HLA-DRw13-Dw18 and DQw6-Dw18, but these antigens did not confer susceptibility in patients whose disease converted to the polyarticular form. HLA-DPw2.1 was an additional susceptibility factor for patients with JA of pauciarticular onset. In the polyarticular form of JA, HLA-DPw3 was the major factor for susceptibility, giving a relative risk of 10.3 (P less than 0.0001). In addition, we found that DRw8.1 and DQw4 were increased, and HLA-DR4 was markedly decreased, in patients with pauciarticular and polyarticular disease. These results indicate that in addition to some shared factors, distinct HLA class II alleles are important in pauciarticular or polyarticular JA. We conclude that typing with oligonucleotide probes may be useful in predicting the outcome in some children with arthritis.

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.

A distinct HLA-DRw8 haplotype characterizes patients with juvenile rheumatoid arthritis

We studied the first domain of the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci of 67 HLA-DRw8-positive Caucasians including 43 with early-onset pauciarticular juvenile rheumatoid arthritis (EOPA-JRA, alternatively known as early-onset pauciarticular juvenile chronic arthritis). Serology, restriction fragment length polymorphism (RFLP), and polymerase chain reaction (PCR) oligotyping revealed that 62, including all the EOPA-JRA patients, carried the HLA-DRB1*0801, DQA1*0401, DQB1*0402 genotype. Approximately one-fifth of the controls carried atypical HLA-DRB1, HLA-DQA1, and/or HLA-DQB1 loci on their HLA-DRw8 haplotype confirmed by family studies. DNA sequences of HLA-DRB1, DQA1, and DQB1 alleles in patients and controls were identical to those previously reported. Disease association studies in 113 EOPA-JRA patients and 207 controls unselected for HLA-DRw8 revealed that the HLA-DRB1*0801, DQA1*0401, DQB1*0402 genotype was associated with a higher relative risk (RR) for disease (RR = 12.8, chi 2 = 48.8, P less than 10(-4)) than was the serologically defined presence of HLA-DRw8 (RR = 8, chi 2 = 39, P less than 10(-4)). Further analysis suggested that the DQ genes on HLA-DRw8 haplotypes are as likely as the DR genes to contribute to the pathogenesis of EOPA-JRA. This study increases to five the number of HLA-DR/DQ haplotypes identified in HLA-DRw8 Caucasians.

HLA-D region genes associated with autoantibody responses to histidyl-transfer RNA synthetase (Jo-1) and other translation-related factors in myositis

Myositis has been associated with HLA-B8 and DR3, especially in white patients with polymyositis and serum anti-Jo-1 antibodies. Twenty-eight patients with myositis and serum translation-related autoantibodies anti-Jo-1, anti-PL-7, anti-PL-12, anti-KJ, and anti-SRP were studied for HLA class II specificities by Southern blotting with HLA-DR beta, DQ beta, and DQ alpha probes. The association of HLA-DR3 (DRw17) with anti-Jo-1 antibodies in white myositis patients was confirmed (P = 0.003, relative risk 8.9). However, HLA-DRw52 haplotypes, regardless of subtype, were present in all of the white and black patients with serum anti-Jo-1 and other translation-related autoantibodies. Moreover, one anti-Jo-1 positive patient had HLA-DRw8, an HLA-DRw52 haplotype on which the DR beta 3 gene has been partially deleted. No HLA-DQ specificity or allele was common to all patients. The HLA-DR3, DR5, DRw6, and DRw8 haplotypes, which bear the HLA-DRw52 specificity, share the most homology in the DR beta 1 first hypervariable region at amino acid positions 9-13. Thus, this DR beta 1 region appears to be the most likely candidate "epitope" for translation-related autoimmune responses in inflammatory myositis.

Major histocompatibility complex class II-restricted antigen presentation across a species barrier: conservation of restriction determinants in evolution

The existence of at least three alleles of the HLA-DRB3 gene within the human population is evident. These alleles express DRw52 determinants and react with monoclonal antibody (mAb) 7.3.19.1. The polymorphic epitope recognized by 7.3.19.1 is not only present on human cells but is also expressed on chimpanzee (Pan troglodytes) class II-positive cells. The 7.3.19.1 determinant already existed before speciation of man and chimpanzee, and is at least 5,000,000 yr old. Two-dimensional gel electrophoresis demonstrated that the various HLA- and Patr-DRw52 molecules that are reactive with 7.3.19.1 exhibit isoelectric point differences due to primary amino acid heterogeneity, as was confirmed by sequencing data. Sequence comparison allowed us to map the binding site of mAb 7.3.19.1 to the alpha helix of the major histocompatibility complex (MHC) class II DRB1 domain surrounding the antigen-binding cleft. Despite MHC sequence variation, chimpanzee antigen-presenting cells can present antigen (purified protein derivative) to human T cell lines and vice versa. Only the HLA- and Patr-DRw52 molecules were shown to function as restriction elements for antigen presentation across this species barrier. It is concluded that these particular restriction determinants probably have been conserved in evolution. The HLA- and Patr-DRw52 molecules represent alleles displaying polymorphism that has been selected for in evolution. Such "biomutants" may thus be more useful to study the biological significance of MHC molecules than MHC variants that have been generated by in vitro mutagenesis experiments.

Association of primary sclerosing cholangitis with HLA-DRw52a

We sought to determine whether there are specific HLA haplotypes in patients with either primary sclerosing cholangitis or primary biliary cirrhosis. Surprisingly, 100 percent of the 29 patients with primary sclerosing cholangitis had the HLA-DRw52a antigen, which is normally present in 35 percent of the population (relative risk, 109.5; P less than 0.00001). Fifteen of these patients had a single common haplotype: A1,B8,Cw7,DRw17,DQw2,DRw52a. In the remaining 17 patients there was a loss of at least one of these antigens. Of the 15 patients with the common haplotype, 12 also had ulcerative colitis, thereby linking the occurrence of ulcerative colitis in patients with primary sclerosing cholangitis to the presence of this haplotype. Although there was no association in 35 patients between primary biliary cirrhosis and specific HLA haplotypes, there was a significant association of the disease with DRw8 (relative risk, 3.1; P = 0.02). We conclude that the development of primary sclerosing cholangitis involves a strong genetic predisposition. Since the association of primary sclerosing cholangitis with HLA-DRw52a appears to be total, HLA typing should be helpful in differentiating this disease from primary biliary cirrhosis.

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.

Transcription and messenger RNA processing upstream of bacteriophage T4 gene 32

Bacteriophage T4 gene 32 lies at the 3' end of a complex transcription unit which includes genes 33, 59, and several open reading frames. In the course of an infection, four major transcripts are synthesized from this unit: two overlapping polycistronic transcripts about 3800 and 2800 nucleotides in length, and two monocistronic gene 32 transcripts about 1150 and 1100 nucleotides in length. These transcripts are made at different times in infection and the polycistronic transcripts have segmental differences in stability. Messenger RNA processing yields a 1025 nucleotide monocistronic gene 32 transcript, and a 135 nucleotide transcript containing part of the gene 59 coding sequence. Processing depends on Escherichia coli encoded ribonuclease E. This pattern of transcription and processing leads to the synthesis of gene 32 mRNA throughout infection, whereas transcripts encoding the upstream genes are present only early in infection. The 3800 nucleotide polycistronic transcript initiates at a promoter that does not require T4 encoded factors for activity. However, full-length synthesis of this transcript depends on the T4 mot gene product. The region upstream of gene 32 also contains four E. coli-like promoters that are active on chimeric plasmids in uninfected cells, but inactive in bacteriophage T4. The location of these cryptic T4 promoters is intriguing in that they lie near the 5' ends of open reading frame B, gene 59 and gene 32. They could play a role in phage development under particular conditions of growth or in bacterial hosts other than those examined here.

Molecular analysis of the HLA-DR5 haplotype

A panel of eleven HLA-DR5 homozygous lymphoblastoid cell lines was investigated for structural heterogeneity on the product level. HLA class II antigens were isolated by immunoprecipitation with different anti-class II monoclonal antibodies and separated by two-dimensional (2-D) gel electrophoresis. As a result, three distinct DRB1, one commonly expressed DRB3, and two distinct DQ gene products could be identified that combined to four different haplotypes associated with HLA-DR5. A hitherto serologically undetected split of HLA-DRw11 was presented by three cell lines. HLA-DRw11 and HLA-DRw12 were found to be related allospecifities that differ only in their DRB1 locus products, but are closely associated with the supertypic DRB3 allele HLA-DRw52b and with HLA-DQw7. The DRB3 alleles HLA-DRw52a and DRw52c were not detected in our cell line panel, indicating that these supertypic determinants are in negative linkage disequilibrium with HLA-DR5. Our data suggest that intra HLA-DR/DQ crossing-over events contribute to the development of the HLA class II polymorphism. Evidence is presented that the T cell defined HLA-D allospecifities are commonly determined by DRB1 and DQ gene products.

Primarily chronic progressive and relapsing/remitting multiple sclerosis: two immunogenetically distinct disease entities

HLA class II gene polymorphism was investigated in 100 patients with clinically definite multiple sclerosis (MS) by restriction fragment length polymorphism analysis of Taq I-digested DNA using DRB, DQA, and DQB cDNA probes. Twenty-six patients had primarily chronic progressive MS and 74 had relapsing/remitting MS. The latter group included patients with a secondary progressive evolution of symptoms. Both clinical forms of MS were found to be associated with the DRw15,DQw6 haplotype. In addition, primarily chronic progressive MS was positively associated with the DQB1 restriction fragment pattern seen in DR4,DQw8, DR7,DQw9, and DRw8, DQw4 haplotypes, as well as negatively associated with the Taq I DQB1 allelic pattern corresponding to the serological specificity DQw7. Relapsing/remitting MS was positively associated with the DQB1 allelic pattern observed in the DRw17,DQw2 haplotype. These three DQB1 alleles are in strong negative linkage disequilibria with DRw15. The two susceptibility markers of each clinical form of MS act additively in determining the genetic susceptibility, as the relative risks for individuals carrying both markers roughly equal the sum of respective risks. Different alleles of the DQB1 locus defined by restriction fragment length polymorphisms contribute to susceptibility and resistance to primarily chronic progressive MS as well as to susceptibility to relapsing/remitting MS. The observed immunogenetic heterogeneity between the different clinical forms of MS favors the hypothesis that primarily chronic progressive MS and relapsing/remitting MS are two distinct disease entities.

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.

Typing for HLA-DPB1*03 and HLA-DPB1*06 using allele-specific DNA in vitro amplification and allele-specific oligonucleotide probes. Detection of "new" DPB1*06 variants

DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes has recently been reported. The resulting DNA amplification was specific for the HLA-DPB locus. Typing for the individual DPB alleles was exclusively dependent on the hybridizations of the probes but hampered by close sequence homology between different DP alleles yielding complex patterns of reactivity with a panel of probes. We report the combined use of allele-specific DNA in vitro amplification and allele-specific oligonucleotides in typing for DPB1*03 and DPB1*06. Complete concordance with PLT typing was observed for the DPB1*03 alleles, while in the DPB1*06 group, at least three variant DPB1*06 alleles were identified which have not been described previously.

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.

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

A third allele at the DRB3 locus, DRw52c, represents an intermediate sequence between DRw52a and DRw52b and may have arisen by a gene conversion-like event. The recognition of cells bearing these molecules by a number of alloreactive and antigen-specific DR-restricted T cell clones was analyzed. On the basis of a theoretical model of HLA class II structure, distinct amino acid clusters have been identified as motifs controlling TCR recognition. These are located both in the cleft and in the alpha-helical edge of the MHC class II recognition platform. Motifs shared between two alleles may restrict public T cell clones.

A method of HLA class II typing using nonradioactive labelled oligonucleotides

The typing of HLA class II genes using molecular biology techniques has brought undoubtedly new insights in the analysis of their polymorphism. Particularly interesting is the dot-blot analysis of enzymatically-amplified genomic DNA hybridized with sequence-specific oligonucleotides. In order to use this technique of typing on a routine basis, we established a non-radioactive detection method of enzymatically-amplified genomic DNA dot-blots. We could clearly demonstrate that, using biotin-labelled specific oligonucleotides, it was possible to specifically discriminate between DQB1 first domain DNA sequences displaying three, two or even only one base-pair difference at a given codon position. The very satisfactory sensitivity level reached by this non-radioactive detection method could safely allow its use for clinical applications of HLA typing at the DNA level.

DNA typing of an HLA-DR bilocus specificity by gene amplification and oligonucleotide hybridization

The structure of the DRB1*03 gene has been interpreted as the product of a gene conversion event involving a DRB3 gene as donor and resulting in the introduction of two short segments of the DRB3 sequence into the DRB1 locus. The serological counterpart of this double insertion is the TR81 specificity. Consequently, the TR81-specifying sequences can reside on either DRB1 or DRB3, or on both loci. Within each of the two sequence stretches a single nucleotide may be responsible for the generation of the TR81 alloantigen. Oligonucleotide probes corresponding to these stretches and to their allelic variants were constructed. They were used, under stringent hybridization conditions, to detect TR81-specifying sequences in the DNA of HLA-homozygous cell lines carrying different haplotypes of the DRw52 family. Prior to hybridization the DNA was amplified with either DRB1-specific or DRB3-specific primers. Using this approach it was possible to perform a "DNA typing" of the TR81-specifying sites separately on both the DRB1 locus and the DRB3 locus.

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.