Mapping SB in relation to HLA and GLO1 using cells from first-cousin marriage offspring

Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus)

BACKGROUND

The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian species, it is notably different among ruminants due to a chromosomal inversion that splits MHC type II genes into two subregions (IIa, IIb). Recombination rates are reportedly high between these subregions, and a lack of linkage has been documented in domestic ruminants. However, no study has yet examined the degree of linkage between these subregions in a wild ruminant. The white-tailed deer (Odocoileus virginianus), a popular ruminant of the Cervidae family, is habitually plagued by pathogens in its natural environment (e.g. Haemonchus contortus, Elaeophora). Due to the association between MHC haplotypes and disease susceptibility, a deeper understanding of MHC polymorphism and linkage between MHC genes can further aid in this species' successful management. We sequenced MHC-DRB exon 2 (IIa) and MHC-DOB exon 2 (IIb) on the MiSeq platform from an enclosed white-tailed deer population located in Alabama.

RESULTS

We identified 12 new MHC-DRB alleles, and resampled 7 alleles, which along with other published alleles brings the total number of documented alleles in white-tailed deer to 30 for MHC-DRB exon 2. The first examination of MHC-DOB in white-tailed deer found significantly less polymorphism (11 alleles), as was expected of a non-classical MHC gene. While MHC-DRB was found to be under positive, diversifying selection, MHC-DOB was found to be under purifying selection for white-tailed deer. We found no significant linkage disequilibrium between MHC-DRB and MHC-DOB, suggesting that these loci are unlikely to be closely linked.

CONCLUSIONS

Overall, this study identified 12 new MHC-DRB exon 2 alleles and characterized a new, non-classical, MHC II gene (MHC-DOB) for white-tailed deer. We also found a lack of significant linkage between these two loci, which supports previous findings of a chromosomal inversion within the MHC type II gene region in ruminants, and suggests that white-tailed deer may have a recombination hotspot between these MHC regions similar to that found for Bos taurus.

Polymorphism of the human retinoid X receptor beta and linkage disequilibrium with HLA-DPB1

The human retinoid X receptor beta (RXRB) gene is localized in the major histocompatibility complex (MHC) region between DPB1 and RING2. The RXRB gene sequence reported by different investigators suggests that the gene may be polymorphic. In this study, we confirmed one polymorphism by sequencing genomic DNA from four Caucasian individuals. We also developed a restriction fragment length polymorphism (RFLP) analysis to detect this specific polymorphism. Linkage analysis studies between RXRB alleles and a number of HLA markers showed significant linkage disequilibrium between RXRB*T and HLA-DPB1*0401.

HLA-DPB1 typing by polymerase chain reaction amplification with sequence-specific primers

DPB1 is the second most polymorphic class II locus with currently 84 recognized alleles, i.e. DPB1*0101 to DPB1*8101. Most of the alleles have been described during the last few years using oligonucleotide and sequencing techniques and relatively little is known about the role and importance of the polymorphic residues as regards to the function of DP molecules. In the present study, polymerase chain reaction (PCR) primers were designed for identification of all the phenotypically different DPB1 alleles by PCR amplification with sequence-specific primers. Forty-eight standard genomic PCR reactions per sample were performed in order to achieve this resolution. Unique amplification patterns were obtained in 2983 of 3160 (94.4%) possible genotypes. The primers were combined so that only very rare genotypes gave rise to ambiguous patterns. Sixty-four Histocompatibility Workshop cell lines and 150 DNAs provided by the UCLA DNA exchange were investigated by the DPB1 primer set. All typing results were conclusive. Analysis of the distribution of DPB1 alleles was performed in 200 Caucasian samples, 100 African samples and 40 Oriental samples. The population study by the DPB1 PCR-SSP method showed a characteristic distribution of HLA-DPB1 alleles. Each ethnic group had one, or two, frequent DPB1 allele(s) and the frequency of homozygotes was high, suggesting that balancing selection does not appear to be affecting the evolution of the DPB1 locus.

The biological significance of HLA-DP gene variation in haematopoietic cell transplantation

Although it has been over 25 years since HLA-DP was mapped to the major histocompatibility complex (MHC), its biological functions remain ill-defined. We sought to test the hypothesis that HLA-DP functions in a manner similar to that of other class II genes by measuring the risk of clinically severe grades III-IV acute graft-vs.-host disease (GVHD) associated with recipient HLA-DP disparity after haematopoietic cell transplantation. HLA-DPB1 exon 2 was sequenced in 205 patients who underwent transplantation from HLA-A, -B, -C, -DRB1 and -DQB1 allele-matched unrelated donors. HLA-DPB1 mismatched recipients experienced a significantly increased risk of acute GVHD compared with HLA-DP-identical transplants. Patients who were mismatched for a single HLA-DPB1 allele had an odds ratio (OR) of 1.0 (0.5, 2.2; P = 0.99) and patients who were mismatched for two alleles had an OR of 2.2 (1.0, 4.9; P = 0.06) for developing acute GVHD. Compared with matched and single-allele mismatched transplants, patients who were mismatched for two DPB1 alleles had an OR of 2.2 (1.2, 4.1; P = 0.01). HLA-DP plays an important role in the alloimmune response. A threshold effect of multiple HLA-DP disparities is evident in determining the risk of acute GVHD after haematopoietic cell transplantation from unrelated donors.

Localization of the recombination points in a family with two DR/DP recombinations

In a family with a maternal DR/GLO recombination, cellular DP typing showed it to be located between DR and DP. RFLP studies done during the 9th international histocompatibility workshop gave anomalous segregation patterns of DPA and DPB bands that could be interpreted as being due to a second, paternal DR/DP recombination. This assumption was confirmed later by PCR-SSO typing. A more precise mapping has been done by new markers showing the maternal recombination to be within the TAP2 locus and the paternal recombination to be between DQB1 and DQB3. This supports earlier suggestions of a hot spot of recombination in the TAP region. The recombinations involve parental haplotypes that presently show DR/DP linkage disequilibrium in the French population and it is proposed that DR/DP recombinations occur randomly while B/DR recombinations preferentially occur on haplotypes without strong linkage disequilibrium. Existing DR/DP linkage disequilibria in a given population will thus be broken down with time. The mixed lymphocyte culture response towards an isolated DP difference was tested in this and another DR/DP recombinant family. It showed that an alloresponse towards DP may be highly variable and this suggests that it might be important to define the rules for the strength of this reaction and the possible implications for allotransplantation.

Frequency of HLA-DPB1 alleles in a Spanish population: their contribution to rheumatoid arthritis susceptibility

HLA-DPB1 allele frequencies in 181 unrelated control individuals and 70 rheumatoid factor-positive RA patients from Seville (Spain) were determined using oligonucleotide typing methods. All frequencies shown concern the percentage of individuals positive for a certain allele. HLA-DPB1*0401 was the most common DPB1 allele in the healthy individuals, possessed by 65.7% of them. In addition to HLA-DPB1*0401, only the following alleles were found in normal subjects at frequencies greater than 10%: DPB1*0101 (15.5%), DPB1*0201 (12.2%), DPB1*0301 (16.6), and DPB1*0402 (29.3%). When HLA-DPB1 allelic frequencies were compared between seropositive RA patients and controls, a negative association for DPB1*0301 and DPB1*0401 was found in RA patients, although it failed to reach statistical significance after correction for the number of comparisons made. The other DPB1 alleles exhibited almost identical frequencies in both groups. However, when only DR4+ patients and controls were considered, the decrease in the frequency of the DPB1*0301 and DPB1*0401 alleles lacked statistical significance. On the other hand, when DR4- RA patients and controls were compared, the frequency of DPB1*0301 was found decreased significantly again, even more than in the whole group of patients.

Linkage disequilibrium within the HLA complex does not extend into HLA-DP

It is well known that certain alleles from different loci within the Human Leucocyte Antigen (HLA) complex are in linkage disequilibrium. This linkage phenomenon is relatively well characterized for haplotypes that include specific class I and class II alleles such as HLA-B8 and HLA-DR3. However, the HLA-DP genes are located at the centromeric end of the HLA complex and are less well characterized with regard to linkage disequilibrium. The availability of a large population of healthy subjects and sequence-specific oligonucleotide (SSO) typing enabled us to assess the degree of linkage between HLA-DPB1 and HLA-DQB1 genes. Using the polymerase chain reaction and a series of oligonucleotide probes which define seven DQ beta alleles and twenty DP beta alleles, we studied 180 unrelated, normal Caucasian individuals and found only weak or negative associations between HLA-DPB1 and HLA-DQB1. These data demonstrate that the association between HLA-DQ and DP is weak and also imply that DP extended haplotypes related to particular diseases may not reflect normal associations. Implications of these results might impact on the concept of linkage disequilibrium in general as well as the evolution of the HLA complex. In addition, extensions of this work may have clinical ramifications with regard to bone marrow transplantation and founder effects in certain diseases.

HLA-DP polymorphism in northern Italian celiac patients

The contribution of HLA-DP genes to celiac disease susceptibility has been investigated in 95 Italian patients, 41 with childhood and 54 with adult disease onset. Polymerase chain reaction amplification, sequence-specific oligonucleotide probe hybridization and restriction fragment length polymorphism analyses have been carried out. All celiac patients and 56 out of 128 random healthy controls were DQw2-positive. The frequency of the DPB1*0101 allele was significantly increased (pc = 0.002, relative risk 5.21) in patients with celiac disease (23.2%) compared to the whole panel of controls (5.5%), but not to the 56 controls bearing DQw2 (10.7%). No significant difference in the frequency of DPB1*0101 was found between celiac patients with pediatric (24.4%) or adult (22.2%) onset. The DPB1*0101 allele was associated with both the DR3-DQw2 and DR7-DQw2 haplotypes. Moreover, our study has not confirmed the association with DPB1*0402 and DPB1*0301 previously reported in celiac children from southern Italy. The linkage of the DPB1*0101 allele with the DQ locus and the observation that the DP but not the DQ association appears to be ethnically dependent strongly support a secondary role of DP molecules in celiac disease susceptibility.

Family study on HLA-DPB1 polymorphism: Linkage analysis with HLA-DR/DQ and two “new” alleles

An extensive family study on HLA-DPB1 was performed in 105 families living in northeastern Japan. In a linkage study between HLA-DPB1 and other HLA loci, five apparent recombinations between DPB1 and DR/DQ loci were observed. The recombination frequency (theta) with maximum probability was estimated to be 0.017 by the lod score method. DPB1 allele and haplotype frequencies in unrelated parents were determined by direct counting. The most common allele was DPB1*0501 with the frequency of 41.2% and the second was DPB1*0201 with 24.0%. Nine DPB1-DR and six DPB1-DQ haplotypes were in significant linkage disequilibrium. Seven kinds of extended haplotypes were observed to be over 1%, in which the most common haplotype A24-B52-DR15-DQ6-DPB1*0901 occurred at 6.0%. Moreover, we found two "new" DPB1 alleles in this study. The first one possesses a single base substitution from DPB1*0501 resulting in an amino acid change. The other is most likely to be formed by an intraexonic recombination between DPB1*0301 and DPB1*0501.

Linkage disequilibrium between DPA1 and DPB1 alleles among Norwegian Caucasoids and Japanese

Associations between alleles at the DPA1 and DPB1 loci were analyzed in 181 Norwegian caucasoids. Associations were observed between the DPA1*0201 and the DPB1*0101, *0901, *1001 and *1101 alleles. An association between DPA1*0201 and the DPB1*0901 allele was also observed among 23 healthy Japanese and 24 Japanese MS patients. In addition, it appeared that among Japanese the DPA1*0201 allele may be associated to the DPB1*0501. In conclusion, alleles at the DPA1 and DPB1 loci display different associations among Norwegian caucasoids and Japanese.

Frequency of HLA-DPB1 alleles, including a novel DPB1 sequence, in the Northern Ireland population

HLA-DPB1 allele frequencies in 150 unrelated normal individuals from Northern Ireland were determined using oligonucleotide typing methods. HLA-DPB1*0401 was the most common allele in the population possessed by 75.3% of subjects, followed by DPB1*0201 (20.7%). In addition to these alleles, only HLA-DPB1*0402, -DPB1*0301, and -DPB1*0501 were present in subjects at frequencies greater than 10%. The results in this study are in broad agreement with other Caucasoid studies, but there is regional and ethnic variation in HLA-DP allele frequencies. Three DPB1 alleles were found to be in linkage disequilibrium with HLA-DR antigens determined by RFLP, namely, DPB1*0101 with DRw17 (Dw24 associated) RFLP, DPB1*0501 with DRw13-Dw19 RFLP, and DPB1*1901 with DRw13-Dw18 (Dw25 associated) RFLP. One individual revealed a novel DPB1 pattern of probe reactivity, which following DNA sequencing was found to be HLA-DPB1*2001. To assess the system used and to compare consistency of results between laboratories, 62 cell lines were oligotyped for HLA-DP. The results revealed the system described here to be extremely accurate and showed excellent agreement of HLA-DP typing results for cell lines between laboratories.

Severe acute graft-versus-host disease by HLA-DPB1 disparity in recombinant family of bone marrow transplantation between serologically HLA-identical siblings: an application of the polymerase chain reaction-restriction fragment length polymorphism method

It has remained to be established that matching of the HLA-DP antigen plays a key role in bone marrow transplantation (BMT), mainly due to the difficulty of the primed lymphocyte test (PLT) method for DP typing. We previously reported an efficient technique for HLA class II genotyping, by digestion of polymerase chain reaction (PCR)-amplified genes with restriction fragment length polymorphisms (RFLP) endonucleases (PCR-RFLP method). DNAs from 46 recipients and corresponding donors in serologically HLA-identical sibling-BMT cases were DP typed by this PCR-RFLP method. Of the 46 cases, five (10.9%) were genetically DP mismatched (recombinant frequency between the DR-DQ and DP subregions was at least 2.7% per meiosis), providing an important opportunity to look at the effect of the disparity only seen in the DP antigen on BMT. Three of the four DP-mismatched BMT cases that could be evaluated developed severe acute graft-versus-host disease, suggesting that DP disparity played an important role in BMT.

Positive correlation between oligonucleotide typing and T-cell recognition of HLA-DP molecules

The identification of 19 different HLA-DPB1 sequences implicates the existence of more DP specificities than can be typed for with cellular methods. How many of the DP beta sequences can be specifically recognized by T cells, and which of the polymorphic regions can contribute to the specificity of allorecognition, is not known. In order to investigate the distribution and the immunological relevance of recently described DPB1 alleles, we have typed a panel of 98 randomly selected Dutch Caucasoid donors for the HLA-DPB1 locus by oligonucleotide typing. Comparison of the typing results with primed lymphocyte typing (PLT) defined DP specificities shows an extremely good correlation. Moreover, additional alleles could be defined by oligonucleotide typing reducing the number of DP blanks in the panel. By selecting the appropriate responder stimulator combinations we were able to show that distinctive PLT reagents against oligonucleotide defined specificities DPB1*0401, DPB1*0402, DPB1*0901, and DPB1*1301 can be generated. To investigate in more detail which part of the DP molecule is responsible for the specificity of T-cell recognition, T-cell clones were generated against HLA-DPw3. The clones were tested for the recognition of stimulators carrying DPB1 alleles which had been defined by oligonucleotide typing and sequence analyses and which differed in a variable degree from DPB1*0301. The recognition patterns demonstrated that differences of one amino acid in polymorphic regions situated either in the beta sheets or alpha helix of the hypothetical model of the HLA class II molecule can eliminate T-cell recognition. Furthermore, sequence analyses revealed a new DPB1 allele designated DPB1*Oos.

Distribution of HLA class II alleles among Norwegian Caucasians

We report genomic HLA class II typing of 181 randomly selected Norwegian controls. Seventeen DRB1, 7 DQA1, 10 DQB1, 2 DPA1, and 16 DPB1 alleles were found in the tested population. HLA class II antigen and allele frequencies are given, as well as the distribution of DRB1, DQA1, DQB1 haplotypes. Linkage disequilibrium between some DPB1 alleles and DRB1 and/or DQB1 alleles are also reported.

Rapid HLA-DPB typing using enzymatically amplified DNA and nonradioactive sequence-specific oligonucleotide probes

A simple and rapid method for characterizing the polymorphism at the HLA-DPB1 locus has been developed. The procedure involves the selective amplification of the polymorphic second exon of the DPB1 locus by the polymerase chain reaction (PCR), followed by hybridization of the amplified DNA with 15 nonisotopic sequence-specific oligonucleotide probes. There are no sequences within the second exon of the DPB1 locus that uniquely define an allele; rather, each allele appears to arise from the shuffling of a limited number of polymorphic nucleotide sequences in six regions of variability. Consequently, individual alleles are identified by the pattern of hybridization of the 15 probes. Two formats for typing are described. In Format I (the dot-blot), the amplified DNA is ultraviolet (UV) cross-linked to a nylon membrane and hybridized with the oligonucleotide probes which are covalently labeled with horseradish peroxidase (HRP). In Format II (the reverse dot-blot), the oligonucleotides, which have poly-T tails, are bound to the membrane and the immobilized array of probes is hybridized to the PCR product which has incorporated biotinylated primers during the amplification process. In both formats, hybridization is detected by a simple colorimetric reaction. The application of this technology to the fields of tissue typing and individual identity is discussed.

Analysis of HLA-DP in HLA-DR/GLO recombinant families and in the population of south-western France

The existing estimates of the recombination fraction between DR and DP are quite variable and often based on anecdotal observations. We have estimated the DR/DP crossover frequency on the basis of families typed for HLA markers and GLO. The frequency of DR/GLO crossing over was 8.7% (23/264 informative meioses), maternal recombinations being about twice as frequent as paternal ones. Of 17 DR/GLO recombinant families typed for DPw1-6, DP was informative in 11 (13 recombinations) but only one of these gave rise to a DR/DP crossover. According to these data the DR/DP recombination fraction is below 1%, in contrast to some earlier published materials. HLA-DR/DP haplotypic associations on 127 informative Caucasoid haplotypes have been evaluated. In agreement with previous studies, DR3 was positively associated with DPw1 and, in addition, DR7 was found to be positively associated with DP-blank (not DPw1-6). The rare DPw6 allele is possibly associated with the DR4, Dw14 allele. The DR-DP haplotype profiles suggest other associations which might become significant if larger materials are tested. The frequency of DP alleles in a random material (N = 201) was found to be in accordance with most of the previously published frequences on European Caucasoids with DPw4 as the predominating frequency (gene frequency 40%) and a blank frequency of 27%.

Structural analysis of the HLA-DR, -DQ, and -DP alleles on the celiac disease-associated HLA-DR3 (DRw17) haplotype

Celiac disease is strongly associated with the HLA class II D-region serologic markers DR3 (DRw17) and DQw2. Moreover, by restriction fragment length polymorphism analysis, greater than 90% of DR3 (DRw17), DQw2 celiac disease patients have a polymorphic 4.0-kilobase Rsa I DP B gene DNA fragment. The present study sought to determine if there is a unique HLA class II D-region A or B gene structural variant on the DR3 (DRw17) haplotype found in celiac disease. The polymorphic second exons of the coding DRB, DQA and DQB, and DPA and DPB genes in celiac disease patients with the DR3 (DRw17) haplotype were sequenced after amplification by the polymerase chain reaction. To define the DP B genes associated with celiac disease, the second exons of the coding DP B genes from 27 celiac disease patients were amplified similarly and probed by using a panel of sequence specific oligonucleotides. The HLA-DR, -DQ, and -DP A and B gene second exon sequences of celiac disease patients were noted to be identical to sequences that can be found also, although at a significantly lower frequency, in unaffected individuals. This is compatible with a disease model wherein the HLA class II genes on the DR3 (DRw17) haplotype are necessary, but not sufficient, for the phenotypic expression of celiac disease. Analysis of the DP B genes revealed a significant increase in the frequency of the alleles DPB1 and DPB3 in celiac disease. Furthermore, the increased frequency of the 4.0-kilobase Rsa I DP B gene restriction fragment length polymorphism in celiac disease can be accounted for by the overrepresentation in disease of the alleles DPB1 and DPB3. The HLA-associated susceptibility to celiac disease appears to be multigenic, with specific, but structurally normal, allelic variants in the DP and DQ/DR subregions contributing to disease susceptibility.

HLA-DP typing by analysis of DNA restriction fragment length polymorphisms in the HLA-DP beta subregion

HLA class II antigens are encoded in the HLA-D region and are highly polymorphic. Southern hybridization technique was used to analyze restriction fragment length polymorphisms (RFLPs) in the DP beta gene and an attempt was made to correlate these with DP haplotypes derived from primed lymphocyte typing (PLT) analysis. Digestion of DNA from 32 Epstein-Barr virus (EBV)-transformed cell lines (of haplotypes DPw2, DPw3, DPw4, DPw5, and Cp63) with three different restriction endonucleases. Southern transfer, and hybridization to the DP beta cDNA probe revealed multiple fragments in all cell lines tested. The polymorphic patterns of these fragments were found to correlate with DP haplotypes, suggesting the possibility that the analysis of DNA RFLPs (DNA typing) in the HLA-DP beta subregion can distinguish and identify HLA-DP haplotypes.

Linkage relationships in the bovine MHC region. High recombination frequency between class II subregions

Class II genes of the bovine major histocompatibility complex (MHC) have been investigated by Southern blot analysis using human DNA probes. Previous studies revealed the presence of bovine DO beta, DQ alpha, DQ beta, DR alpha, and DR beta genes, and restriction fragment length polymorphisms for each of these genes were documented. In the present study, the presence of three additional class II genes, designated DZ alpha, DY alpha, and DY beta, are reported. DZ alpha was assumed to correspond to the human DZ alpha gene while the other two were designated DY because their relationship to human class II genes could not be firmly established. The linkage relationships among bovine class II genes and two additional loci, TCP1B and C4, were investigated by family segregation analysis and analysis of linkage disequilibrium. The results clearly indicated that all these loci belong to the same linkage group. This linkage group is divided into two subregions separated by a fairly high recombination frequency. One region includes the C4, DQ alpha, DQ beta, DR alpha, and DR beta loci and the other one is composed of the DO beta, DY alpha, DY beta, and TCP1B loci. No recombinant was observed within any of these subregions and there was a strong or fairly strong linkage disequilibrium between loci within groups. In contrast, as many as five recombinants among three different families were detected in the interval between these subregions giving a recombination frequency estimate of 0.17 +/- 0.07. The fairly high recombination frequency observed between class II genes in cattle is strikingly different from the corresponding recombination estimates in man and mouse. The finding implies either a much larger molecular distance between some of the bovine class II genes or alternatively the presence of a recombinational "hot spot" in the bovine class II region.

An extended HLA-D region haplotype associated with celiac disease

Celiac disease has one of the strongest associations with HLA (human leukocyte antigen) class II markers of the known HLA-linked diseases. This association is primarily with the class II serologic specificities HLA-DR3 and -DQw2. We previously described a restriction fragment length polymorphism (RFLP) characterized by the presence of a 4.0-kilobase Rsa I fragment derived from an HLA class II beta-chain gene, which distinguishes the class II HLA haplotype of celiac disease patients from those of many serologically matched controls. We now report the isolation of this beta-chain gene from a bacteriophage genomic library constructed from the DNA of a celiac disease patient. Based on restriction mapping and differential hybridization with class II cDNA and oligonucleotide probes, this gene was identified as one encoding an HLA-DP beta chain. This celiac disease-associated HLA-DP beta-chain gene was flanked by HLA-DP alpha-chain genes and, therefore, was probably in its normal chromosomal location. The HLA-DP alpha-chain genes of celiac disease patients also were studied by RFLP analysis; 84% of HLA-DR3, -DQw2 patients had a 16-kb Xba I fragment that was present in only 36% of HLA-DR3, -DQw2 controls. Moreover, 79% of these patients had both alpha- and beta-chain polymorphisms in contrast to 27% of controls. Thus, celiac disease is associated with a subset of HLA-DR3, -DQw2 haplotypes characterized by HLA-DP alpha- and beta-chain gene RFLPs. Within the celiac-disease patient population, the joint segregation of these HLA-DP genes with those encoding the serologic specificities HLA-DR3 and -DQw2 indicates: (i) that the class II HLA haplotype associated with celiac disease is extended throughout the entire HLA-D region, and (ii) that celiac-disease susceptibility genes may reside as far centromeric on this haplotype as the HLA-DP subregion.

Molecular analysis of HLA-DP specificities HLA-DPw1, -DPw2 and -DPw4: DP beta chain heterogeneity correlates with PLT subtyping

HLA-DP molecules were isolated from Epstein-Barr virus transformed B cell lines by immunoprecipitation with monoclonal antibody B7/21.2 and subsequently analysed by two-dimensional gel electrophoresis. The results obtained demonstrate that the HLA-DP molecules that can be isolated from cells positive for the HLA-DP specificities HLA-DPw1, -DPw2 and -DPw4 display DP beta chain isoelectric point differences, whereas no DP alpha chain polymorphism was observed. These results suggest that the PLT defined HLA-DP specificities (HLA-DPw1, -DPw2 and -DPw4) are probably DP beta chain structures.

Genetic recombination within the human T-cell receptor alpha-chain gene complex

Genetic analyses of the human T-cell receptor (TCR) alpha-chain genes indicate that recombination events may occur frequently within this gene complex. Examination of the inheritance of restriction fragment length polymorphisms (RFLP) detected by using probes for constant or variable region gene segments made it possible to assign TCR alpha haplotypes to the 16 parents and 43 offspring of eight families studied. A total of six RFLP, three for the constant region and three for variable region gene segments, were examined in the present studies. Most enzyme and probe combinations tested revealed no polymorphism and those finally selected for the study showed limited polymorphism in that only two or, in one case, three allelic forms of the gene were seen. In spite of limited variability at this level, extensive heterogeneity was observed for the combinations of markers present in haplotypes, suggesting that frequent recombination events have occurred. Most strikingly, multiple combinations of RFLP occurring in close proximity of the TCR alpha constant region gene were observed in this study. A high recombination frequency for the TCR alpha gene complex is further supported by the observation that two children, one in each of two families, inherited recombinant TCR alpha haplotypes.

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.

Differential expression of DRw52-like determinants detected by monoclonal antibodies

The reactivity of three monoclonal antibodies (MoAb) directed against DRw52-like determinants was studied in relation to the reactivity of an anti-DR MoAb using fluorescence-activated cell sorter (FACS) analysis. The MCS-7 MoAb reacted with all DRw52+ cells and in addition with DR2+, DR4+, and a DR7+ cell. Both the I-LR2 and the 7.3.19.1 MoAb reacted with DR3+, DR5+, and DRw6+ cells only. However, whereas the 1-LR2 MoAb reacted strongly with all those cells compared with the anti-DR MoAb, the 7.3.19.1 MoAb reacted strongly with DR3+ cells only, and somewhat less with DR5+ and DRw6+ cells. The implications of this for the location of DRw52-like determinants on DR beta chains is discussed.

Mapping of the class II region of the human major histocompatibility complex by pulsed-field gel electrophoresis

The class II region of the human major histocompatibility complex (MHC) encodes a polymorphic set of cell surface glycoproteins involved in the regulation of the immune response. Each glycoprotein is a heterodimer composed of a alpha-chain of relative molecular mass (Mr) 34,000 (34 K) and a beta-chain of Mr = 28K. The products of the class II region have been characterized by the mixed lymphocyte reaction, serology, primed lymphocyte typing and DNA cloning. DR, DQ and DP, three subregions containing both alpha- and beta-chains, and two additional loci, DZ alpha and DO beta, locate this gene cluster on the short arm of chromosome 6. The precise genomic organization of these loci have been difficult to determine. Here we describe the use of pulsed-field gel electrophoresis together with restriction endonucleases having few genomic restriction sites and Southern blotting, to determine the order of the subregions and to derive a map for the human class II region. The order of these loci is similar to that of the homologous loci in the murine class II region. Our study establishes the use of pulsed-field gel electrophoresis in mapping large regions of the genome in higher eukaryotes.

DO beta: a new beta chain gene in HLA-D with a distinct regulation of expression

The HLA-D region of the human major histocompatibility complex encodes the genes for the alpha and beta chains of the DP, DQ and DR class II antigens. A cDNA clone encoding a new class II beta chain (designated DO) was isolated from a library constructed from mRNA of a mutant B-cell line having a single HLA haplotype. Complete cDNA clones encoding the four isotypic beta chains of the DR1, DQw1, DPw2 and putative DO antigens were sequenced. The DO beta gene was mapped in the D region by hybridization with DNA of HLA-deletion mutants. DO beta mRNA expression is low in B-cell lines but remains in mutant lines which have lost expression of other class II genes. Unlike other class II genes DO beta is not induced by gamma-interferon in fibroblast lines. The DO beta gene is distinct from the DP beta, DQ beta and DR beta genes in its pattern of nucleotide divergence. The independent evolution and expression of DO beta suggest that it may be part of a functionally distinct class II molecule.

The genomic organisation and nucleotide sequence of the HLA-SB(DP) alpha gene

We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizing fragments, we constructed lambda and cosmid libraries of human DNA and screened them at low stringency with the HLA-DR alpha gene specific subclone. We have isolated clones corresponding to each of the six fragments and, in this paper, describe those which contain the gene encoding HLA-SB(DP) alpha.

Recognition of DP determinants with typing reagents prepared with lymphocytes from Dutch unrelated individuals

In an attempt to make our own set of DP typing reagents, we used lymphocytes from 12 unrelated donors, who were all HLA-A1,2; B7,8; DR2,3; DQW1,2. They all had been previously typed for DP using a reference set of well established reagents obtained from Dr. S. Shaw (NIH, Bethesda). Thirty-six promising responder-stimulator combinations were primed in bulk MLC and tested for their specificity in secondary MLC. All reagents gave reaction patterns which were concordant with the sensitizing DP types, with the exception of those combinations where a donor was used in which DR2 appeared to be associated with a non-DW2 HLA-D type. Over 1,200 reactions obtained with the new reagents were compared with those obtained with the established ones, in six different experiments. High correlation coefficients (r values) were found between the two kinds of reagents. The typings of a panel of individuals with the reference set and with our new typing set revealed an excellent agreement for DP assignments with the two sets, with the exception of the specificity DP4. The DP gene frequencies for random Dutch Caucasoids were defined.

Implication of structural class II gene polymorphism for the concept of serologic specificities

We have used DNA-DNA hybridization methods to study the relationship of genetic polymorphisms to the established HLA-D region determinants as detected with serological reagents. The supertypic determinants DRw52 and 53 are closely associated with a particular RFLP detected with the DR beta probe, but are seemingly encoded by a distinct beta gene compared to the "conventional" DR antigens. DQw1 is closely associated with a DQ alpha chain polymorphism, whereas the DQw2 and 3 specificities have correlations to RFLP using the DQ beta probe. Additional DQ polymorphism, in linkage disequilibrium with DR but yet without a serological counterpart is also described. Considering the finding that there exist a varying number of DR beta genes in different DR haplotypes (Böhme et al. 1985), from 1 in DRw8 to 3 (or 4) in DR4- and DR7-positive cells, we have made a tentative re-evaluation of the genetic basis for the conventional DR specificities. The combination of cell surface antigens encoded by DR and DQ loci are believed to form the basis for MLC stimulating determinants. We have speculated that a combination of determinants encoded by distinct DR beta genes and in certain instances additional DQ polymorphism is responsible for the DR types. Thus, only a limited variability is observed after DNA-DNA hybridization using DR beta probes. Only DR1-, 2- and 4-positive cells have distinct bands not detected in any other haplotypes, whereas DR3, 5, w6, and w8 can be characterized by a combination of bands, which is the result of hybridization with several DR beta genes. Furthermore, we have suggested that the difference between the DR3 and DRw6 specificities is due to variability with regard to 1 DQ beta gene, and have also made the assumption that DRw6 cells may express a lower concentration of DR locus encoded products compared to DR3-positive cells (Haziot et al. 1985). In addition, we have discussed the genetic basis for so-called DR blanks, implying that an unorthodox combination of DR and DQ determinants forms the basis for difficulties in assigning DR types to such cells in some cases and that "blanks" can be associated with low expression at the cell surface of well-known DR determinants. The use of cDNA and genomic probes for distinct class II genes to elucidate the mechanisms of HLA and disease association has been documented and discussed.

SB subregion of the human major histocompatibility complex: gene organization, allelic polymorphism and expression in transformed cells

The SB region of the human major histocompatibility complex (MHC) has been cloned from cosmid and lambda phage libraries made from the human B-lymphoblastoid cell line Priess (DR4/4, DC4/4, SB3/4). Two alpha genes and two beta genes are encoded in the 100 kb long SB region in the order SB alpha-SB beta-SX alpha-SX beta. The SB alpha and SB beta genes encode the alpha and beta subunits of the SB subset of class II MHC molecules. Both the SX alpha and the SX beta genes are pseudogenes in the haplotype examined. From the isolated clones, the two haplotypes of the Priess cell line, SB3 and SB4, are distinguished by nucleotide sequencing and blot hybridization analyses. Restriction site polymorphisms between the SB3 and SB4 clones were observed only in relatively small regions of the SB beta and SX beta genes. A mouse macrophage cell line was transfected with one of the cosmid clones containing both SB alpha and SB beta genes. Expression of the alpha and beta genes was detected by fluorescene-activated cell sorting (FACS) and two-dimensional gel electrophoresis using SB-specific monoclonal antibodies.

Relation of insulin-dependent diabetes mellitus (IDD) and the HLA-linked SB system

This report deals with the question of the susceptibility for IDD association with the recently described HLA-linked SB system. The SB system is located centromeric of HLA-DR between HLA-DR and GLO. At present five specificities of the SB system, which behave as alleles, can be recognized. A total of 40 IDD patients and 96 normal controls were characterized for HLA-A, -B, -C, -DR and SB antigens. Our results confirmed the strong positive association of IDD with HLA-DR3 and -DR4 and the negative association of IDD with HLA-DR2. The genetic analysis of the SB system and IDD, however, demonstrated no significant association between alleles of SB and susceptibility for IDD. The analysis of association between alleles of HLA-DR and SB revealed no significant linkage disequilibrium in IDD patients and a significant linkage disequilibrium between SB1 and HLA-DR3 in the controls. These results suggest that the genes associated with susceptibility for IDD are primarily coded for telomeric of SB and tightly linked with HLA-DR.