Structure, sequence and polymorphism in the HLA-D region

HLA-OLI: A new MHC class I pseudogene and HLA-Y are located on a 60 kb indel in the human MHC between HLA-W and HLA-J

Analysis of publicly available whole-genome sequence data from the Human Pangenome Project and the 1000 Genomes Project has identified a DNA segment of approximately 60 kb in the major histocompatibility complex (MHC) between HLA-W and HLA-J that is present in some MHC haplotypes but not others. This DNA segment is largely repeat element-rich but includes the pseudogene HLA-Y, thus pinpointing the location of this pseudogene, and a new HLA class I sequence we have called HLA-OLI. HLA-OLI clusters phylogenetically with the HLA class I pseudogenes, HLA-P and HLA-W, and appears to have a similar genetic structure. The availability of whole-genome sequence data from diverse populations enables a detailed characterization of the MHC at the population level and will have implications for understanding MHC disease associations and the non-HLA MHC factors that impact unrelated hematopoietic cell transplant outcomes.

Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures

Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.06%-0.49% in a 1000 Genomes Project read remapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.

LAG3 and Its Ligands Show Increased Expression in High-Risk Uveal Melanoma

Uveal melanoma (UM) is a rare ocular malignancy which originates in the uveal tract, and often gives rise to metastases. Potential targets for immune checkpoint inhibition are lymphocyte-activation gene 3 (LAG3) and its ligands. We set out to analyse the distribution of these molecules in UM. The expression of mRNA was determined using an Illumina array in 64 primary UM from Leiden. The T lymphocyte fraction was determined by digital droplet PCR. In a second cohort of 15 cases from Leiden, mRNA expression was studied by Fluidigm qPCR, while a third cohort consisted of 80 UM from TCGA. In the first Leiden cohort, LAG3 expression was associated with the presence of epithelioid cells (p = 0.002), monosomy of chromosome 3 (p = 0.004), and loss of BAP1 staining (p = 0.001). In this Leiden cohort as well as in the TCGA cohort, LAG3 expression correlated positively with the expression of its ligands: LSECtin, Galectin-3, and the HLA class II molecules HLA-DR, HLA-DQ, and HLA-DP (all p < 0.001). Furthermore, ligands Galectin-3 and HLA class II were increased in monosomy 3 tumours and the expression of LAG3 correlated with the presence of an inflammatory phenotype (T cell fraction, macrophages, HLA-A and HLA-B expression: all p < 0.001). High expression levels of LAG3 (p = 0.01), Galectin-3 (p = 0.001), HLA-DRA1 (p = 0.002), HLA-DQA1 (p = 0.04), HLA-DQB2 (p = 0.03), and HLA-DPA1 (p = 0.007) were associated with bad survival. We conclude that expression of the LAG ligands Galectin-3 and HLA class II strongly correlates with LAG3 expression and all are increased in UM with Monosomy 3/BAP1 loss. The distribution suggests a potential benefit of monoclonal antibodies against LAG3 or Galectin-3 as adjuvant treatment in patients with high-risk UM.

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

A simple electronic tool for assessing amino acid sequence polymorphisms within exon-2 of HLA-DPB1 alleles

In November 2014, the OPTN/UNOS Board of Directors mandated that HLA-DPB1 typing be performed for all deceased donors. Currently, there are over 1,000 known HLA DPB1 alleles, yet fewer than 30 are represented on commonly used single antigen bead (SAB) solid phase antibody assays. Moreover, the official World Health Organization (WHO) nomenclature for the DPB1 locus does not permit assessment of structural relationships between alleles based on their names. Thus, for donor DPB1 alleles lacking a corresponding SAB, determining the compatibility between a donor-recipient pair when the recipient possesses DPB1 antibodies currently requires the use of manual sequence alignments. Multiple studies have reported that DPB1 alleles can be classified into serological-defined categories based on shared protein sequence motifs residing in distinct hypervariable regions. To date, six such motifs have been recognized. To address this problem, we developed a computer-assisted tool to compare donor and recipient DPB1 allele sequences, specifically those defined by DPB1 hypervariable region motifs located in exon 2 (http://dpreport.hlatools.org). This tool quickly identifies mismatched DPB1 motifs, and easily permits the identification of motif-based donor-specific antibodies (DSA) to DPB1.

Naming HLA diversity: A review of HLA nomenclature

The development of a standardized HLA nomenclature has been critical in our understanding of the HLA system and in facilitating the clinical applications of HLA. The Nomenclature Committee for Factors of the HLA System, established in 1968, has overseen the development and usage of nomenclature based on serologic specificities, cellular responses, and DNA sequences. Their decisions have been guided by community consensus reached through 17 international workshops beginning in 1964 and continuing today. Two websites provide a curated database of the sequences of over 26,000 HLA alleles and a reference site for the current nomenclature. This review covers the major steps in the development of the HLA nomenclature as well as the efforts of other groups to extend its usefulness for research and clinical applications.

Human leukocyte antigen matching in organ transplantation: what we know and how can we make it better (Revisiting the past, improving the future)

PURPOSE OF REVIEW

A renaissance for human leukocyte antigen (HLA) testing emerged with the understanding that donor-specific HLA antibodies play a significant role in long-term allograft survival. This renewed focus on donor/recipient histocompatibility led to a recent quest to decipher antibody responses or, as introduced into the transplantation lexicon, 'HLA-epitope matching'.

RECENT FINDINGS

Whether matching is at the antigen or the epitope level, in-depth understanding of how histo-incompatibility leads to activation of an immune response is required. HLA-DQ donor-specific antibody (DSA) has the highest association with poor graft survival. However, HLA-DQ antigens and antibodies are understudied and significant gaps still exist in understanding the function of HLA-DQ in immune activation. Much of our knowledge about HLA class-II molecules is derived from studies performed on HLA-DR, whether it is crystallography, antigen processing and presentation analysis, or activation of T-cell signal-transduction pathways. Indeed, HLA-DQ molecules are less amenable for laboratory testing, but the limited studies that were performed indicate that HLA-DQ might have, at least to some extent, a different role compared with HLA-DR.

SUMMARY

This review highlights qualities of HLA-DQ that may be associated with different pathways of activating an immune response. Understanding the consequences of such differences may lead to better appreciation and significance of HLA-DQ for matching purposes.

Poor correlation between T-cell activation assays and HLA-DR binding prediction algorithms in an immunogenic fragment of Pseudomonas exotoxin A

The ability to identify immunogenic determinants that activate T-cells is important for the development of new vaccines, allergy therapy and protein therapeutics. In silico MHC-II binding prediction algorithms are often used for T-cell epitope identification. To understand how well those programs predict immunogenicity, we computed HLA binding to peptides spanning the sequence of PE38, a fragment of an anti-cancer immunotoxin, and compared the predicted and experimentally identified T-cell epitopes. We found that the prediction for individual donors did not correlate well with the experimental data. Furthermore, prediction of T-cell epitopes in an HLA heterogenic population revealed that the two strongest epitopes were predicted at multiple cutoffs but the third epitope was predicted negative at all cutoffs and overall 4/9 epitopes were missed at several cutoffs. We conclude that MHC class-II binding predictions are not sufficient to predict the T-cell epitopes in PE38 and should be supplemented by experimental work.

A Mathematician's Odyssey

In this overview of my research, I have aimed to give the background as to how I came to be involved in my various areas of interest, with an emphasis on the early phases of my career, which largely determined my future directions. I had the enormous good fortune to have worked under two of the most outstanding scientists of the twentieth century, R.A. Fisher and Joshua Lederberg. From mathematics and statistics, I went to population genetics and the early use of computers for modeling and simulation. Molecular biology took me into the laboratory and eventually to somatic cell genetics and human gene mapping. One chance encounter led me into the HLA field and another led me into research on cancer, especially colorectal cancer. On the way, I became a champion of the Human Genome Project and of the need for scientists to help promote the public understanding of science.

HLA-DQ barrier: effects on cPRA calculations

BACKGROUND

Panel-reactive antibody (PRA) testing provides assessment of the breadth of sensitization a patient might have against human leukocyte antigen (HLA) antigens. The evolution of calculated PRA (cPRA) reflects the commitment of the transplant community to increase accessibility and promote equity to all patients awaiting kidney transplantation. Recent data from our center and others, however, suggested that a significant diversity of HLA-DQ antigens is not captured, which may lead to inequity in allocating cPRA points.

METHODS

HLA-DRB1-DQA1-DQB1 typing of 2182 individuals was evaluated for this study using Luminex-based sequence-specific oligonucleotide typing. A total of 3182 haplotypes were confirmed to have the level of resolution required for this study.

RESULTS

The diversity of HLA-DQαβ alleles is greater than what is apparent using the serologic equivalents. The distribution of these alleles within a serologic group varies, with some alleles being more frequent than others; therefore, their representation within the current cPRA system is inaccurate. Three informative examples are given. Haplotypes of DR antigens with DQαβ alleles did not always follow the common published linkage disequilibrium, especially in populations where there is greater genetic diversity.

CONCLUSIONS

The current cPRA system does not take into account the distribution of molecular equivalents within DQ serologic specificities. This can result is inequitable allocation of sensitization points and disadvantaging the more sensitized patients. To ameliorate this situation, the United Network for Organ Sharing system should allow inputting HLA-DQαβ alleles both for donor typing and as antibody specificities, which will lead to better representation of unacceptable DQ alleles and improve organ allocation equity.

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

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

Mixed lymphocyte culture studies reveal complexity in the bovine MHC not detected by class I serology

The genetic structure of the bovine major histocompatibility complex (MHC) was investigated using the lymphocyte microcytotoxicity test for class I typing and the mixed lymphocyte culture (MLC) assay for class II typing. Using locally produced alloantisera and antisera from the Third International BoLA Workshop, 14 class I BoLA-A locus alleles were identified in the study population, a single herd of approximately 700 Holstein-Friesian cattle. Eleven of these were alleles recognized in the International Workshop and three were new alleles. An MLC titration assay was employed in conjunction with class I typing to define BoLA haplotypes and identify BoLA complex homozygotes. An embryo transfer family consisting of eight full sibling cattle including one BoLA complex homozygote was produced by half sibling mating. Five other BoLA complex homozygotes were subsequently identified in the herd. Six MLC defined class II haplotypes investigated in detail were designated BoLA-D1, D2, D3, D4, D5 and D7. BoLA-D1 was associated with the class I specificity BoLA-Aw6, D2 with Aw6 and the new class I specificity Ac3, D3 with Aw6 and Aw11, D4 with Aw10, D5 with Aw31 and Aw11, and D7 with Aw20. The discovery of four groups of class I identical-class II disparate haplotypes, and three pairs of class I disparate-class II identical haplotypes indicates the presence of considerable complexity in the BoLA complex that is not detected using class I serology.

Identification of genetic variation in the bovine major histocompatibility complex DR beta-like genes using sequenced bovine genomic probes

Two bovine genomic clones that crosshybridize with HLA-DR beta cDNA have been isolated. Nucleotide sequence analysis of the beta 1, beta 2 and transmembrane (TM) exon regions for one of these clones revealed 70, 89 and 86% identity with the corresponding HLA-DR beta exons. Stop codons are present in the beta 1 and TM exons and a single base deletion toward the 3' end of the TM exon negates the consensus sequence for exon/intron splicing. Therefore, we conclude this is a bovine DR beta-like pseudogene, BoDR beta I. Exon-containing regions have been used as probes in Southern blot analyses of bovine genomic DNA digested with EcoRI. The beta 2 exon of BoDR beta I results in prominent bands of 18.9, 7.8, 7.2, 6.4, 5.6, 3.6, 3.0 and 2.7 kb. Polymorphisms were observed for all but the 18.9 kb band and at least three of these bands were identified in each of the 185 animals sampled. A probe containing the TM exon of BoDR beta I hybridizes only to the 5.6- and 3.6-kb bands, suggesting that these are allelic bands corresponding to this pseudogene. Results from hybridizations of a TM exon-containing probe of the second bovine DR beta-like clone (BoDR beta II) suggest that the 6.4- and 2.7-kb bands correspond to this second bovine gene. A nonpolymorphic 8.1-kb band results from a probe containing the BoDR beta I beta 1 exon. Major differences in frequency for the 6.4/2.7 alleles were found for the four breeds sampled.

Class II major histocompatibility complex genes of the sheep

The class II genes of the sheep major histocompatibility complex (MHC) have been cloned from two unrelated heterozygous sheep into cosmid vectors. By restriction mapping and hybridization with a number of class II probes of human and mouse origin, the cloned genetic material has been assigned to seven distinct alpha genes, 10 distinct beta genes and 14 beta-related sequences. It was difficult to identify homologues of specific HLA class II genes because of a tendency for the ovine genes to cross-hybridize between HLA probes representing different loci. Such cross-hybridization was especially marked among the beta genes. While DQ and DR homologues have been tentatively identified by several criteria, no genes corresponding to DP have been identified. Cosmids containing class II alpha and beta genes have been transfected into mouse LTK- cells, and surface expression of a sheep class II molecule has been obtained.

Genomic hybridization of bovine class II major histocompatibility genes: 1. Extensive polymorphism of DQ alpha and DQ beta genes

Class II genes of the bovine major histocompatibility complex (MHC) were investigated by Southern blot analysis using human cDNA probes for DQ alpha, DQ beta, DR alpha and DR beta. The presence of a DQ-like and a DR-like subregion in cattle was clearly indicated. Highly polymorphic restriction fragment patterns were obtained when genomic DNA, digested with any one of the BamHI, EcoRI or PvuII restriction enzymes, was hybridized with the DQ alpha and the DQ beta probe. The polymorphisms were interpreted genetically by analysing five paternal half-sib families of the Swedish Red and White breed. The material comprised, besides the bulls, 28 offspring and their dams. The analysis resolved 9 and 12 allelic variants of DQ alpha and DQ beta respectively. Thus, this investigation establishes a method for routine typing of MHC class II gene polymorphism in cattle. The results were entirely consistent with close linkage of DQ alpha and DQ beta since no recombinant was found and since alleles at these loci occurred in complete linkage disequilibrium in the material investigated. Close linkage between DQ and the blood group locus M, which has previously been found to be closely linked to the serologically defined BoLA-A locus, was also indicated. In this study DNA was isolated from frozen semen samples of dead bulls, which shows that this type of analysis will be useful in genetic investigations in cattle breeds, where artificial insemination is practised.

Genomic hybridization of bovine class II major histocompatibility genes: 2. Polymorphism of DR genes and linkage disequilibrium in the DQ-DR region

Class II genes of the bovine major histocompatibility complex have been investigated by Southern blot analysis using human cDNA probes for DQ alpha, DQ beta, DR alpha and DR beta. In this report restriction fragment length polymorphisms of DR alpha and DR beta are described. The polymorphisms were interpreted genetically by analysing five paternal half-sib families of the Swedish Red and White Breed, comprising altogether 28 offspring. Using the restriction enzymes BamHI, EcoRI and PvuII, three DR alpha and three DR beta allelic fragment patterns were resolved. The DR alpha and DR beta genes thus appear to be much less polymorphic than the previously described DQ alpha and DQ beta genes. Also, the observed linkage disequilibrium between DR genes was less pronounced than that between DQ genes, whereas the association between DR and DQ haplotypes was very strong. The family data available indicated strongly that the DQ alpha, DQ beta, DR alpha and DR beta genes are all closely linked.

The molecular genetics of HLA-related disorders

The HLA region on the short arm of chromosome 6 contains a set of highly polymorphic loci responsible for regulating the immune response. Particular haplotypes, defined serologically, have been associated with a risk of developing certain autoimmune diseases such as insulin-dependent (juvenile-onset) diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Recent developments in molecular biology have permitted an improved resolution of the locus and of the sequential arrangement of the susceptibility determinants on these haplotypes. Restriction fragment length polymorphisms have allowed subdivisions of serological haplotypes to be made. These correlate with disease susceptibility in some cases. Amplification of specific HLA class II alleles and nucleic acid sequencing have resulted in the identification of the structural determinants in the HLA that underlie some of these diseases.

Sequence-based typing of HLA class II DQB1

Due to the expanding number of known HLA class II DQB1 alleles, high-resolution oligotyping is becoming ineffective, therefore a sequence-based typing (SBT) strategy was developed to provide rapid and definitive typing of HLA-DQB1. HLA-DQB1*02, *03, *04, *05, and *06 alleles were individually amplified by polymerase chain reaction (PCR) using exon 2 group-specific primers. Forward and reverse PCR primers were tailed with M13 universal and M13 reverse sequences, respectively. Subsequent bi-directional cycle-sequencing was carried out using Cy5.5-labeled M13 universal primer and Cy5.0-labeled M13 reverse primer. Automated sequencing was performed in 30 min using a Visible Genetics, Inc. (VGI) MicroGene Clipper Sequencer. Full concordance was observed between this SBT method and oligotyping among 151 individuals.

Heterogeneity of HLA-DR2 haplotypes in Caucasoid Americans, African Americans, Chinese Americans, Native Americans and Xiamen Chinese

HLA-DR, -DQ specificities were determined by PCR amplification with SSOP in 4560 individuals: Caucasoid Americans (CA), African Americans (AA), Chinese Americans (ChA), Native Americans (NA) and Xiamen Chinese (XC). DR2 subtypes were compared amongst the five ethnic populations. The DRB1*1501-DRB5*0101 haplotype was found to be the most frequent in all populations except African Americans, in which DRB1*1503-DRB5*0101 was the predominant haplotype, accounting for 65% of DR2 subtypes. In contrast to Caucasoid Americans, the DRB1*1602 is strongly associated with the DRB5*0101 allele in Chinese populations. The presence of DRB5*0203 and DRB1*1602-DRB5*0101 haplotypes in Chinese populations, especially in Xiamen Chinese, suggests that various DR2 haplotypes may be generated via multiple gene conversion events together with point mutations and reciprocal recombination. The strong DR and DQ associations are found in DRB1*1501/DQB1*0602 (66.22%) for CA, DRB1*1503/DQB1*0602 (56.58%) for AA, DRB1*1501/DQB1*0602 (30.20%) and DRB1*1602/DQB1*0502 (15.76%) for ChA, DRB1* 1501/DQB1*0602 (41.55%) and DRB1*1602/DQB1*0301 (40.25%) for NA, and DRB1*1501/DQB1*0602 (30.26%) and DRB1*1602/DQB1*0502 (25.81%) for XC.

Analysis of the human HLA-DRA gene upstream region: evidence for a stem-loop array directed by nuclear factors

Sequence analysis of the far-upstream region of the human HLA-DRA gene has revealed the presence of Y' and X' boxes, highly homologous to the well characterized Y and X boxes present within the proximal-promoter region. Comparison of Y, Y', X, and X' box sequences present within different class II MHC genes of different species demonstrates that these boxes are conserved during evolution, suggesting an important role in regulation of gene expression. The far-upstream region and the proximal promoter region of the class II MHC genes could be organized in secondary structures, as suggested for the EA gene, the murine counterpart of the human HLA-DRA gene. The essential feature of this model is a dimerization of the proteins binding to X and X' and/or Y and Y' boxes resulting in a loop-out of the intervening DNA and a rapprochement of the far-upstream and proximal-promoter regions, and consequently of any proteins binding to them. We set up an in vitro approach in order to determine whether proteins bound to sequences present within far-upstream and proximal-promoter regions of the human HLA-DRA gene could direct a secondary structure assembly of regulative regions. Moreover, by gel retardation and DNase I footprinting assays, we demonstrate that similar proteins bind to Y and Y' boxes and, among these proteins, NF-Y was unambiguously identified by antibody-super shift experiments. Taken together, the data presented in this paper provide evidence supporting the hypothesis that a stem-loop array of the 5'-upstream region of the human HLA-DRA gene could be directed by nuclear factors. In this manner, additional nuclear factors bound to the far region could be driven in close proximity of the transcription initiation site.

High-resolution HLA typing for the DQB1 gene by sequence-based typing

The ideal high-resolution typing strategy for polymorphic genes is sequence-based typing. SBT of genomic DNA has been developed for the HLA class II genes DRB1, DRB3/4/5 and DPB1. For the DQB1 gene the sequence-based typing method was shown to cause a number of problems. To resolve those problems, different primers to amplify and sequence exon 2 of DQB1 were designed and tested. With several primer combinations, preferential amplification was observed in individuals heterozygous for DQB1*02/*03 and DQB1*02/*04. The preference was for DQB1*02 in many instances but could also be demonstrated for DQB1*03 or *04 and resulted occasionally in allelic drop-out. The best primer combination was selected and successfully used to type individuals heterozygous for DQB1*02, *03 and *04. To distinguish DQB1*0201 and *0202, primers for amplification and sequencing of exon 3 were developed and correct subtyping was obtained. The ambiguous typing DQB1*0301/*0302 and DQB1*0303/*0304 was resolved by allele-specific amplification and sequencing. A total of 258 individuals were fully typed for their DQB1 subtypes. All samples had been previously typed by PCR-SSP and serology. Concordant typing results were obtained for all individuals tested. The DQB1 alleles detected included *0501, *0502, *0503, *0601, *0602, *0603, *0604, *0609, *0201, *0202, *0301, *0302, *0303, *0304, *0401 and *0402. Sequence-based typing of the DQB1 gene proved a reliable typing strategy for assignment of the different DQB1 alleles after intensive selection of primers and test conditions.

A new HLA-DQB1*0306 allele sharing motifs from DQB1*03032 and DQB1*04 sequences

We have discovered a new HLA-DQB1 allele in a Japanese family, MAT. In the family the new allele segregates in three generations and demonstrates the positive association with DRB1*0901. We observed a novel RFLP pattern in the course of examining the modified PCR-RFLP method for HLA-DQB1 genotyping. The PCR-SSOP analysis also showed a new hybridized pattern. Sequence analysis of the allele indicates that it was generated by a gene conversion-like event between the HLADQB1*03032 and one of DQB1*04 contemporary alleles. This new allelic product did not react with all of allosera and monoclonal antibodies against DQ1, DQ2, DQ3, DQ4 and DQ7. The HLA molecule encoded by the allele is not defined by serology. This new allele was officially recognized and named DQB1*0306 by the WHO Nomenclature Committee in November 1995.

An apparent functional correlation between variations in amino acid residues in HLA-DR4.1 and 4.2 serological subtypes and oligonucleotide characterization

HLA-DR4 can be subdivided serologically into two specificities, DR4.1 and DR4.2, using well-defined monospecific alloantisera used in the 11th International Histocompatibility Workshop. In this study, a total of 1095 random DR4-positive individuals from several ethnic groups were tested first for serotype DR4.1/4.2 and then for DRB1*04 alleles using polymerase chain reaction (PCR) followed by sequence-specific oligonucleotide probe hybridization (SSOPH). An almost 100% correlation between samples testing positive for DR4.1 and the presence of alanine at position 74 was observed, while samples testing positive for DR4.2 correlated with the presence of glutamic acid at position 74. DRB1*04 alleles 0401, 0402, 0404, 0405, 0408, 0409 and 0410 are aligned in functional groups which coincide with the serological subtype of DR4.1. DRB1*04 alleles 0403, 0406, 0407 and 0411 coincide with subtype DR4.2. Amino acid substitutions at positions 57, 71 and 86 indicate other significant variations between alleles within the serological subgroup of DR4.1 and define five minor subgroups. The serologic and oligonucleotide allelic subgroups are in turn correlated with recognized cellular Dw antigens. While sequence data provide evidence of structural differences, data on cellular antigens support a functional association between these designated groups and their significance in transplantation and GVHD. Testing results are categorized by ethnic group in order to establish frequency data for donor selection criteria.

Molecular characterization of major histocompatibility complex class II gene expression and demonstration of antigen-specific T cell response indicate a new phenotype in class II-deficient patients

Major histocompatibility complex (MHC) class II deficiency is an inherited autosomal recessive combined immunodeficiency. The disease is known as bare lymphocyte syndrome (BLS). BLS is characterized by a lack of constitutive MHC class II expression on macrophages and B cells as well as a lack of induced MHC class II expression on cells other than professional antigen-presenting cells (APCs) due to the absence of mRNA and protein of the human leukocyte antigen (HLA) class II molecules, designated HLA-DR, -DQ, and -DP. The defect in gene expression is located at the transcriptional level and affects all class II genes simultaneously. Here we have analyzed transcription and protein expression of class II antigens in Epstein-Barr virus (EBV)-transformed B lymphoblastoid cell lines and mononuclear cells (MNCs) of twin brothers. Whereas flow cytometric analysis failed to detect class II antigens on the cell surface of the patients' EBV-B cells and MNCs, examination of the genes coding for HLA-DR, -DQ, -DP, and the invariant chain (Ii) by reverse transcriptase-polymerase chain reaction amplification resulted in an unusual mRNA pattern in the B cell lines of the patients (HLA-DR alpha +, -DR beta, -DQ alpha +, -DQ beta -, -DP alpha -; -DP beta +, Ii+). In accordance with these findings no HLA-DR beta-specific protein was detected by immunoblotting, whereas low levels of HLA-DR alpha and normal levels of Ii were present. In contrast to EBV-B cells, the MNCs of both patients displayed a residual HLA-DR beta, -DQ beta, and -DP alpha mRNA signal. Furthermore, HLA-DR beta-specific protein was found in addition to HLA-DR alpha by immunoblotting of cell lysates, even though it was clearly decreased as compared with controls. Our results indicate that the defect in class II antigen expression is not necessarily present to the same extent in B cells and cells of other lineages. mRNA levels of HLA-DR beta were found to be enriched in adherent cells within the MNC fraction. Further investigations indicated that the MHC class II expressed is functional in antigen presentation, as the two boys' CD4+ T cells became activated and expressed interleukin-2R after stimulation of peripheral blood mononuclear cell cultures with recall antigen (tetanus toxoid). Furthermore, T cells tested in one of the two patients responded to both MHC class I and II allostimulation, and this response was inhibited by monoclonal antibodies of the respective specificity.(ABSTRACT TRUNCATED AT 400 WORDS)

Association of primary biliary cirrhosis with the allele HLA-DPB1*0301 in a German population

The major histocompatibility complex class II alleles at the HLA-DPB1 locus were investigated in 32 German Caucasoid patients with primary biliary cirrhosis (PBC) and compared with those from 47 normal control patients using molecular genotyping techniques. The second exon of the HLA-DPB1 gene was amplified by polymerase chain reaction (PCR) and hybridized with 25 sequence-specific oligonucleotides (SSOs) to assign the HLA-DPB1 alleles on the basis of known sequence variations, according to the protocols of the Eleventh International Histocompatibility Workshop. A strong association of PBC was found with the allele HLA-DPB1*0301. The allele HLA DPB1*0301 was present in 50% (16 of 32) of the patients with PBC compared with 13% (6 of 47) of normal controls (P corrected < .015), whereas the other HLA-DPB1 alleles showed no significant differences in both groups. The relative risk (RR) estimate for the allele HLA-DPB1*0301 was 6.8 (95% confidence limits: 2.27 to 20.57). In summary, this study clearly demonstrates an association of PBC with the HLA-DPB1*0301 allele in German Caucasoids and may add new data to the immunogenetic background of PBC, suggesting a contribution of the HLA-DPB1 gene to the genetic susceptibility of the disease.

Evolution of Mhc class II polymorphism: the rise and fall of class II gene function in primates

The substitution rate at the codons implicated at ARS of Mhc class II genes has previously been shown to be heavily biased towards nonsynonymous substitutions, indicative of positive selection for polymorphism. Based on our analysis of the number of synonymous changes at codons outside putative ARS in primates, the average age of the polymorphism at class II loci was found to increase in the following order: DPB1, DRB3, DRB5, DRB1, DRB4, DQB1, DQA1. For DRB loci, nonsynonymous changes were found to exceed synonymous changes at HLA-DRB1, DRB3 and DRB5, while no evidence of deviations from equal rates of synonymous and nonsynonymous substitutions were found for DRB6. The pattern of substitutions at the DRB loci of most Catarrhini species indicates constant positive selection at ARS codons over the evolutionary period examined. An exception to the relatively stable selection pattern between species exhibited by most loci is the appearance of polymorphism under positive selection at DRB4 only in the regular chimpanzee. The ds/dn ratios for DQA1 and DQB1 alleles are lower than for the most polymorphic DRB genes. Since the dn/ds ratio of ARS codons may be positively correlated to the ds for non-ARS codons, at least for DQB1, caution must be exercised in interpreting the low ratio for the DQ genes as an indication of weaker selection. The DQA1 allelic lineages show different dn/ds ratios, consistent with the hypothesis that the lineages are constrained from evolving in relation to the diversity of the interacting DQB1 alleles. In contrast to all other class II loci, DPB1 appears to have been subjected to strong positive selection only in the human lineage, and may represent the most conspicuous example of an Mhc locus acquiring an altered function in antigen presentation.

Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism

An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the--corrected--DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201.(ABSTRACT TRUNCATED AT 250 WORDS)

Gel electrophoretic analysis of rhesus macaque major histocompatibility complex class II DR molecules

Rhesus macaque MHC class II DR molecules were isolated from radiolabeled B-cell line extracts by immunoprecipitation with the mAbs 7.3.19.1 and B8.11.2 and subsequently analyzed by 2D-gel electrophoresis. The B-cell lines used for this study were obtained from monkeys that are homozygous for the Mamu-DR region as defined by serologic techniques. Some of these animals have been selectively bred and originate from consanguineous matings. These analyses show that monkeys with the same allotyping may express different types of DR molecules. As in humans, the number of DR molecules expressed per haplotype is not constant and varies from 1 to 3, depending on the serologically defined Mamu-DR specificity, whereas it has been shown that the number of Mamu-DRB genes present per haplotype varies from 2 to 6. Therefore the present study also demonstrates that some of the rhesus macaque DR regions contain one or more pseudogenes.

HLA-DPB1 polymorphisms on the MHC-extended haplotypes of families of patients with Graves' disease: two distinct HLA-DR17 haplotypes

HLA-DPB1 polymorphisms were investigated in 217 members of 21 multiplex families of patients with Graves' disease, who had previously been haplotyped, using in vitro enzymatic DNA amplification and hybridization with sequence-specific oligonucleotide probes. Using the strategy of group-specific amplification, we were able to assign 19 DPB1 alleles with the use of 13 sequence specific oligonucleotide probes. No recombination was found between HLA-DPB1 and the HLA-DR/DQ complex in 243 informative meioses. HLA-DPB1*0401 was found to be the most common allele followed by DPB1*0101, *0201 and 0402 with allele frequencies of 0.4214, 0.1132, 0.1069 and 0.1006, respectively. Besides the strong linkage disequilibrium between HLA-DPB1*0101 allele and the HLA-B8, DR17/DQ2 haplotype; HLA-DPB1*0202 and *1101 alleles were also found to be significantly associated with HLA-B18 and DR7 with Pc < 0.001 and Pc < 0.009, respectively. HLA-DR17/DQ2 was found to be more commonly associated with HLA-DPB1*0101 on the Affected haplotypes (from family members affected with Graves' disease) while associated with DPB1*0401 on the Ab + ve haplotypes (deduced from thyroid autoantibody positive unaffected members). The differences in the frequency of this preferential association on the Affected and Ab + ve haplotypes was statistically significant (ch 2 = 10.18, df = 2, P < 0.007). Though it is rater unlikely that the HLA-DPBI polymorphism by itself could contribute a direct role towards the genetic susceptibility for the development of autoimmune thyroid disease, it could serve as a marker in identifying family members with the HLA-DR17/DQ2 haplotype who are more likely to develop Grave's disease or thyroid autoantibodies.

The marsupial MHC: the tammar wallaby, Macropus eugenii, contains an expressed DNA-like gene on chromosome 1

In the placental mammal major histocompatibility complex (MHC) three main families of class II genes, DR, DQ, and DP, have been recognized. Each family contains genes that code for one or more A- and B-chains. Recent evidence has indicated that a fourth family can be described, the DN/DO family. These four families arose sometime early in mammalian evolution. Our purpose was to deduce the MHC of an early mammalian ancestor of marsupials and eutherians. Using primers designed to conserved regions in exon 2 and exon 3 of the DQA gene we amplified an 830-bp band from the total genomic DNA of the marsupial, Macropus eugenii (tammar wallaby). However, sequence analysis of cloned genomic products showed that the primers had amplified three genes, two of which appeared to be alleles at one locus, while the other gene belonged to a closely related locus. Phylogenetic analysis showed that both these loci were most closely related to the human (HLA-DNA) and mouse (H-20a) DNA genes, with a bootstrap support of 78%. Expression of only one locus could be detected by RT-PCR from spleen RNA. In situ hybridization to tammar wallaby chromosomes mapped these genes to one region on the long arm of chromosome 1, indicating the position of the MHC in marsupials. Related A-chain genes were detected in monotremes, and human by southern blotting, and very faint bands were observed in the chicken. Hybridization with a tammar DNA-like gene on several marsupial species showed evidence of at least three DNA-like loci in the tammar wallaby, at least one in the koala, but none in the kowari. This indicates that the organization of the class II MHC may be more dynamic in marsupial than in placental mammals, but, in contrast to a previous study on the MHC of a marsupial, we cannot conclude that the class II gene families of placental and marsupial mammals evolved from different ancestral genes.

DQA1*03 subtypes have different associations with DRB1 and DQB1 alleles

Polymorphisms outside the hypervariable regions of HLA class II alleles that do not affect the peptide-binding site are probably not under selective pressure and could therefore be useful as markers of the evolutionary pathways of the HLA class II haplotypes. We have analyzed such a polymorphism in the variants of DQA1*03, which differ at residue 160 encoded in exon 3. Our study included homozygous BCLs of the 10th IHWS and samples of a multiracial panel of 723 unrelated subjects which were also typed for allelic variations in exon 2 by hybridization with SSOP. BCLs having DQA1*03 and 131 selected DQA1*03-positive samples were typed for the dimorphism in exon 3 that distinguishes DQA1*0301 and DQA1*0302. DQA1*0301 was found to be exclusively associated with DQB1*0302, while samples carrying DQB1*0201, 0301, 0303, and 0401 always had DQA1*0302. A few haplotypes carrying DQB1*0302 had DQA1*0302. The fact that DQA1*0301 is completely included in DQB1*0302, and not vice versa, suggests that DQA1*0301 may have arisen from a mutation in a haplotype containing DQA1*0302-DQB1*0302. DQB1*0302 was found to be associated with all DR4 subtypes, suggesting possibly that the current variants of DRB1-DR4 may be of more recent origin. DRB1*0405 was the only subtype of DR4 which was not associated with DQA1*0301 and had multiple associations with the DQB1 alleles, therefore, perhaps representing the oldest allele of this group.

Complete association of the HLA-DRB1*04 and -DQB1*04 alleles with Vogt-Koyanagi-Harada's disease

VKH disease is a bilateral panuveitis and has been known to be closely associated with the particular HLA class II antigens HLA-DR4 and -DQ4, defined by serologic typing. In this study, 63 Japanese VKH patients were analyzed for HLA class II alleles at the DNA level using the PCR-RFLP method. The DRB1*04 alleles encoding the serologic specificity DR4 were found in 100% of the VKH patients carrying DRB1*0405 or DRB1*0410. By statistical analysis, only DRB1*0405 was found to be significantly increased as compared to the healthy controls (RR = 46.7 and pc < 1 x 10(-5)). As to the DQB1 locus, all the patients carried DQB1*0401 or DQB1*0402 expressing the serologic DQ4 specificity, which is in a strong linkage disequilibrium with DRB1*0405 or DRB1*0410 in a Japanese population, respectively. Only DQB1*0401 showed a statistically significant increase as compared to the healthy controls (RR = 41.3 and pc < 1 x 10(-5)). Comparison of the amino acid sequences of these DRB1 and DQB1 alleles indicates that Ser at position 57 of DRB1 and/or Glu at position 70 and Asp at position 71 of DQB1 plays a crucial role in determining the susceptibility to VKH disease.

Presence of an expressed beta-tubulin gene (TUBB) in the HLA class I region may provide the genetic basis for HLA-linked microtubule dysfunction

An expressed beta-tubulin gene (TUBB) has previously been localized to chromosome region 6pter-p21 in man. By using a panel of deletion mutant cell lines and radiation-reduced hybrids containing fragments of chromosome 6, the TUBB locus could be mapped to the HLA class I region at 6p21.3. A long range restriction map including TUBB and several HLA class I genes was then generated by rotating field gel electrophoresis. The results show that TUBB maps to a segment 170-370 kb telomeric of HLA-C. This location suggests that a mutation at the TUBB locus could be the cause for certain forms of HLA-linked microtubule dysfunction, including immotile cilia syndrome.

Expression and modulation of class I and class II histocompatibility leukocyte antigens on human soft tissue sarcomas

BACKGROUND

Class I and Class II histocompatibility leukocyte antigens (HLA) play an important role in the antigenic recognition and target cell killing by T-lymphocytes. Their expression and modulation with gamma interferon on human soft tissue sarcomas were investigated.

METHODS

The phenotypic expressions of Class I and Class II HLA were determined by avidin-biotin immunoperoxidase staining using two monoclonal antibodies W6/32 and MEL3, respectively.

RESULTS

The present study showed that soft tissue sarcomas frequently had demonstrable Class I HLA and less-frequently expressed Class II HLA: The staining for Class I HLA was more diffuse, and the staining for Class II HLA was generally patchy in appearance. The expressions of two antigens on cultured sarcoma cells were found in accordance with the findings of sarcoma tumors. The expression of Class I antigen was enhanced, and Class II was induced in two cell lines by gamma interferon. The in vitro modulation of HLA with gamma interferon was reversible. Gamma interferon at the testing dose did not have cytotoxic or antiproliferative effects on either cell lines.

CONCLUSIONS

Through the modulation of HLA on soft tissue sarcomas, gamma interferon may play a role in the clinical management of sarcomas.

Restriction fragment length polymorphism of DQB and DRB class II genes of the ovine major histocompatibility complex

The ovine major histocompatibility complex (MhcOvar) class II region was investigated by Southern blot hybridizations using ovine probes specific for the second exons of Ovar-DRB and Ovar-DQB genes. Multiple bands were revealed when genomic DNA was digested with each of five restriction enzymes (BamHI, EcoRI, HindIII, PvuII and TaqI), and successively hybridized with the two radiolabelled ovine probes. Restriction fragment length polymorphisms (RFLPs) were analysed in 89 sheep originating from six inbred families and the inheritance of the fragment patterns was determined. Forty-one fragments were recorded with the DQB probe; 32 were detected with the DRB probe. They constituted 9 DQB and 10 DRB allelic patterns. Twelve DQB-DRB haplotypes were resolved in this study.

Assignment of HLA-DPB alleles by computerized matching based upon sequence data

Routine HLA typing by serology has been supported by DNA or protein analysis of the respective molecules in cases when serologic typing was inconclusive or difficult to perform. DNA analysis by RFLP, SSO, or PCR amplification with SSP is a reliable tool for the identification of alleles. Because DNA sequences may now be determined routinely, we developed software based on sequence data from known sequences for allele assignment of polymorphic gene systems. We describe the assignment of HLA-DPB alleles based upon sequence data obtained after PCR amplification and subsequent sequencing of exon 2. Our software includes a database containing all known HLA-DPB sequences, which offers the possibility of analyzing heterozygous individuals by combinatorial comparison through all alleles and thus identifying the one or two alleles involved. Quality control of the sequence has been included by the alignment of constant regions of the sequence combined with related polymorphism of known polymorphic nucleotides and the identification of the positions crucial for the allele assignment. The ability to type for HLA-DPB alleles routinely by automatic sequence determination and subsequent automated analysis offers new perspectives for HLA-DNA typing.

Isolation, characterization and evolution of ovine major histocompatibility complex class II DRA and DQA genes

Four full-length ovine major histocompatibility complex (MHC) class II A cDNA clones coding for new alleles of DRA, DQA1 and DQA2 genes were isolated from two ovine lambda gt10 cDNA libraries. The derived amino acid sequences of these clones resemble class II A molecules from other species in both size and structure. Restriction fragment length polymorphism analysis, using an Ovar-DRA probe on DNA from Merino and Romney sheep revealed only limited polymorphism in contrast to the high levels of polymorphism revealed by Ovar-DQA probes. Comparison of the predicted amino acid sequences for the three ovine A genes with class II A genes from five other species revealed that the most variable region of the molecule is the signal peptide. Although virtually every amino acid site shows variation, within or between species, there are some blocks of highly conserved residues. Within gene comparisons of nucleotide differences reveal that the greatest number of changes is found between the alleles of Ovar-DQA1 and -DQA2 genes and the least between Ovar-DRA1 alleles. Phylogenetic analysis of class II A sequences from several species place DRA and DQA genes on two distinct branches, with Ovar-DRA1 and BOLA-DRA, and Ovar-DQA1 and BOLA-DQA being most similar on their respective branches.

Restricted expression of transgenic HLA-DRA gene in thymic epithelial cells and its role in acquisition of T cell tolerance to self-superantigens and processed DR alpha-derived peptide

We have established a set of transgenic mouse lines in which the HLA-DRA gene was expressed in different cell types. In one line (DR alpha-24), DR alpha E beta b molecules were expressed on thymic medullary and cortical epithelial cells and all lineages of bone marrow-derived antigen-presenting cells (APC) except for thymic macrophages. By contrast, expression of the molecules in another line (DR alpha-30) was found on thymic medullary and cortical epithelial cells but not on bone marrow-derived APC in the thymus and periphery. To evaluate the role of thymic epithelial cells in acquisition of T cell tolerance, comparative analysis of DR alpha-24 and DR alpha-30 was performed. In DR alpha-30, T cells expressing TcR V beta 5 and V beta 11 were eliminated to comparable levels to those in DR alpha-24, suggesting that expression of the DR alpha E beta b molecules on thymic epithelial cells are sufficient for clonal deletion of the self-superantigen-reactive T cells. In addition, CD4+ T cells from DR alpha-30 as well as those from DR alpha-24 were tolerant to DR alpha-derived peptide/I-Ab complex expressed on spleen cells from DR alpha-24 even in the presence of exogenous interleukin-2. These observations suggest that expression of the DR alpha chain in thymic epithelial cells could induce T cell tolerance directed toward naturally processed DR alpha-derived peptide bound to I-Ab molecules, probably via clonal deletion of the self-reactive T cells.

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.

Isoelectric focusing subtypes of HLA-A can be defined by oligonucleotide typing

This study describes a simple and direct method for sequence-specific oligonucleotide probe (SSOP) typing of the A locus of HLA class I genes. Genomic DNA from a panel of over 200 cells which have been characterized by the methods of serology and isoelectric focusing (IEF) for the HLA class I antigens was used for locus-specific PCR amplification of HLA-A sequences. Dot blot hybridization of the amplified products was performed with 28 SSOPs derived from hypervariable regions in exon 2 and 3. Co-amplification of three alleles of HLA-H pseudogene in apparent linkage disequilibrium with HLA-A2 and A10 was observed but did not interfere with the typing of HLA-A alleles. Using short SSOPs (15 nucleotides each) in single temperature tetramethylammonium chloride (TMAC) hybridization and washing steps, 30 IEF-definable isotypes of HLA-A antigens could be unambiguously defined by their hybridization patterns. Moreover, comparison of the typing results with available nucleotide sequences of HLA-A alleles showed that the conditions used allowed faithful detection of single codon mismatches between probe and template. Thus, these alleles can be identified by their unique hybridization patterns generated by the SSOPs. Nucleotide sequence analysis of any new HLA-A allele will further permit its rapid and unambiguous characterization by SSOP typing.

Distinct associations of HLA class II genes with inflammatory bowel disease

BACKGROUND

There are relatively few studies of HLA class II association either with Crohn's disease (CD) or ulcerative colitis (UC). The few available association studies have been carried out by serological techniques, and the results from these studies are inconclusive.

METHODS

The association between HLA class II genes was studied using molecular genotyping in combination with allele-specific oligonucleotide hybridization by polymerase chain reactions.

RESULTS

In UC (n = 74), we observed a positive association with the HLA DR2 allele (P = 0.008) and negative associations with the DR4 (P = 0.018) and DRw6 (P = 0.028) when compared with ethnically matched controls (n = 77). No associations were observed with any DQ alleles. In contrast, in CD (n = 95) we observed a positive association with the combination of DR1 and DQw5 alleles (P = 0.021). Furthermore, stratifying DR1 and DQw5 alleles indicated that neither allele was independently associated with CD, suggesting that the association was with the haplotype rather than either of the alleles individually. A suballele of DQw5, DQB1*0501, contributed this haplotypic association (P = 0.012).

CONCLUSIONS

DR and DQ molecules firmly separate UC and CD on genetic grounds, suggesting that the contribution of the HLA class II genes to the disease susceptibility is quite different for the two disorders.

A human monoclonal antibody reacting against HLA-DQ1-, DQ4-, and a subset of DQ7-bearing cells

Human mAb 2A2 recognizes an epitope present in the HLA-DQ1 + 4 specifications and also on several DQ7-positive cells. We have investigated the extra reactions of this monoclonal reagent on a wider panel of DQ1-, DQ4-negative/DQ7-positive B-cell lines. The results obtained support the existence of two subtypes of the HLA-DQ7 specificity on the basis of their reactivity with human mAb 2A2; the DQ7/2A2-positive variant has been found in 12 of 29 BCLs positive for the DR11 antigen, and in four of eight BCLs bearing DR4-DQ7 haplotypes. It has also been detected in the DR12-positive cells assayed and in several unusual DR/DQ7 combinations not commonly found in Caucasoid populations, including the DR13-DwHAG and DR14-Dw16 haplotypes. Results from competition binding assays between 2A2 and well-characterized murine anti-DQ polymorphic mAbs suggest that the epitope recognized by human mAb 2A2 on DQ1- or DQ4-bearing haplotypes is located on the DQ beta chains of such specificities, being amino acid residues 54-55, the potential binding site of antibody 2A2, whereas the binding site on DQ7 antigens cannot be explained on the basis of known amino acid sequences.