Nomenclature for factors of the HLA system, 1995

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.

A gene feature enumeration approach for describing HLA allele polymorphism

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

HLA association in SLE patients from Lahore-Pakistan

The first genetic factors to be identified as important in the pathogenesis of Systemic lupus erythematosus (SLE) were those of the major histocompatibility complex (MHC) on chromosome 6. It is now widely accepted that MHC genes constitute a part of the genetic susceptibility to SLE. The study population comprised 61 SLE patients fulfilling at least four of the American college of Rheumatology criteria for SLE and 61 healthy blood donors as controls. SLE female versus male ratio was approximately 9:1. Mean age at diagnosis was 30.35 ± 1.687 (12-68 years). DNA-based HLA Typing for HLA-A, HLA-B, and HLA-DRB1 was carried out by Polymerase chain reaction with sequence specific primers using genomic DNA obtained from blood samples. A total of 22 alleles have been studied at locus A, 37 alleles at locus B and 17 DRB1 alleles. The allelic frequencies of HLA-A, HLA-B, and HLA-DRB1 antigens in SLE patients from Pakistan were compared with the controls. A significant increase was observed in the frequency of HLA-A*01, A*03, A*11, A*23, A*26 A*69, HLA-B*27, B*40, B*49, B*51, B*52, B*53, B*54, B*95, HLA-DRBI*01, DRBI*03, DRBI*11, DRBI*14 among SLE patients indicating a positive association of these alleles with SLE. HLA-A*24, A*29, A*31, A*34, A*68, A*92, HLA-B*18, HLA-DRB1*12, were found to be decreased in the patient group as compared to controls indicating a negative association of these alleles with SLE. Thus from this study we can conclude that SLE is associated with certain MHC alleles in Pakistani population.

Clinical and HLA phenotypes of type 1 autoimmune hepatitis in North American patients outside DR3 and DR4

AIMS

To determine the clinical phenotype and outcome of patients with definite type 1 autoimmune hepatitis, who lack human leukocyte antigen (HLA) DR3 and DR4, and to assess the importance of HLA DR7 and DR13.

METHODS

Two hundred and seven adult patients were typed for DR3, DR4, DR7, and DR13 by DNA-based techniques. One hundred and two blood donors constituted a normal population.

RESULTS

Twenty-six patients lacked DR3 and DR4 (13%). Treatment failure occurred more commonly in these individuals than in the 68 patients with DR4 (20% vs. 3%, P = 0.03), and relapse after drug withdrawal was less frequent than in the 84 patients with DR3 (55% vs. 87%, P = 0.03). HLA DR13 occurred more often than in those with DR3 (54% vs. 15%, P = 0.0002) or DR4 (54% vs. 12%, P = 0.00005), and it was more frequent than in normal adults (54% vs. 22%, P = 0.003), including those without DR3 or DR4 (54% vs. 27%, P = 0.03). HLA DR7 was not associated with susceptibility or outcome.

CONCLUSIONS

White North American patients who lack DR3 and DR4 respond differently to corticosteroid treatment than patients with classical HLA phenotypes. HLA DR13 is common in these adult patients, and it may affect treatment outcome.

Determination of the HLA-DM interaction site on HLA-DR molecules

HLA-DM removes CLIP and other loosely bound peptides from MHC class II molecules. The crystal structures of class II molecules and of HLA-DM have not permitted identification of their interaction sites. Here, we describe mutations in class II that impair interactions with DM. Libraries of randomly mutagenized DR3 alpha and beta chains were screened for their ability to cause cell surface accumulation of CLIP/DR3 complexes in EBV-B cells. Seven mutations were associated with impaired peptide loading in vivo, as detected by SDS stability assays. In vitro, these mutant DR3 molecules were resistant to DM-catalyzed CLIP release and showed reduced binding to DM. All mutations localize to a single lateral face of HLA-DR, which we propose interacts with DM during peptide exchange.

One third of HLA DQ2 homozygous patients with type 1 diabetes express celiac disease-associated transglutaminase autoantibodies

Type 1 diabetes and celiac disease are both immunologic disorders where specific HLA alleles are associated with disease risk. We have developed a radioassay for autoantibodies to tissue transglutaminase (tTG) following the report that this enzyme is 'the' endomysial autoantigen (EMA) of celiac disease. The radioassay for transglutaminase autoantibodies is similar to that utilized for detecting anti-islet autoantibodies. The 'cut-off' for the IgA autoantibody assay was established as 3 x 100th percentile of 184 healthy control subjects at an index of 0.05. Ninety-eight of 847 patients with type 1 diabetes (11.6%) had tissue transglutaminase autoantibodies (tTG). All EMA-positive patients were positive (49/49) for transglutaminase autoantibodies, as were 49/540 EMA-negative patients. Twenty transglutaminase-positive patients consented to intestinal biopsy and 15 biopsies were positive for celiac disease. All patients with a transglutaminase level greater than 0.70 (13/13) had a positive biopsy, while none (0/3) with a level <0.3 had a positive biopsy. The prevalence of transglutaminase autoantibodies was higher in diabetic patients with HLA DQ2 or DQ8. One third of DQ2 homozygous patients (22/68) expressed transglutaminase autoantibodies vs. less than 2% of patients lacking DQ2 or DQ8. A simple radioassay for IgA transglutaminase autoantibodies detects all endomysial antibody positive patients and detects transglutaminase autoantibodies in 5% of endomysial autoantibody negative patients. The prevalence of transglutaminase autoantibodies is associated with DQ2 and DQ8 and in particular DQ2 homozygosity. Autoimmunity to transglutaminase is remarkably prevalent amongst patients with type 1 diabetes expressing certain class II HLA alleles.

The optimization of helper T lymphocyte (HTL) function in vaccine development

Helper T lymphocyte (HTL) responses play an important role in the induction of both humoral and cellular immune responses. Therefore, HTL epitopes are likely to be a crucial component of prophylactic and immunotherapeutic vaccines. For this reason, Pan DR helper T cell epitopes (PADRE), engineered to bind most common HLA-DR molecules with high affinity and act as powerful immunogens, were developed. Short linear peptide constructs comprising PADRE and Plasmodium-derived B cell epitopes induced antibody responses comparable to more complex multiple antigen peptides (MAP) constructs in mice. These antibody responses were composed mostly of the IgG subclass, reactive against intact sporozoites, inhibitory of schizont formation in liver invasion assays, and protective against sporozoite challenge in vivo. The PADRE HTL epitope has also been shown to augment the potency of vaccines designed to stimulate a cellular immune response. Using a HBV transgenic murine model, it was found that CTL tolerance was broken by PADRE-CTL epitope lipopeptide, but not by a similar construct containing a conventional HTL epitope. There are a number of prophylactic vaccines that are of limited efficacy, require multiple boosts, and/or confer protection to only a fraction of the immunized population. Also, in the case of virally infected or cancerous cells, new immunotherapeutic vaccines that induce strong cellular immune responses are desirable. Therefore, optimization of HTL function by use of synthetic epitopes such as PADRE or pathogen-derived, broadly crossreactive epitopes holds promise for a new generation of highly efficacious vaccines.

Characterization and distribution of Mhc-DPB1 alleles in chimpanzee and rhesus macaque populations

Allelic diversity at the nonhuman primate Mhc-DPB1 locus was studied by determining exon 2 nucleotide sequences. This resulted in the detection of 17 chimpanzee (Pan troglodytes), 2 orangutan (Pongo pygmaeus) and 16 rhesus macaque (Macaca mulatta) alleles. These were compiled with primate Mhc-DPB1 nucleotide sequences that were published previously. Based upon the results, a sequence specific oligotyping method was developed allowing us to investigate the distribution of Mhc-DPB1 alleles in distinct chimpanzee and rhesus macaque colonies. Like found in humans, chimpanzee and rhesus macaque populations originating from different geographic backgrounds appear to be characterized by the presence of a few dominant Mhc-DPB1 alleles.

Mapping of specific and promiscuous HLA-DR-restricted T-cell epitopes on the Plasmodium falciparum 27-kilodalton sexual stage-specific antigen

We have characterized HLA-DR-restricted T-cell epitopes on the 27-kDa protein (Pfg27), a sexual stage-specific antigen, of the human malaria parasite Plasmodium falciparum in subjects with a history of malaria. Pfg27, expressed early in the sexual stages, is recognized by monoclonal antibodies capable of reducing the infectivity of gametocytes in mosquitoes. By using 16 Pfg27-specific CD4(+)-T-cell clones derived from three donors, seven different T-cell epitopes were identified. Among them, P11 (amino acids 191 to 210 of the Pfg27 sequence, IDVVDSYIIKPIPALPVTPD) was found to contain a previously described binding motif for multiple HLA-DR allotypes. Indeed, P11 was found to be promiscuous in that it could be recognized by T cells in the context of at least five different HLA-DR molecules. The cytokine profile of the clones was mixed. Seven of nine T-cell clones exhibited a Th0-like cytokine profile, producing high levels of gamma interferon (IFN-gamma) and interleukin-4 (IL-4) upon stimulation with specific peptides and mitogens. The other two clones had a Th1-like cytokine profile with high expression of IFN-gamma and no IL-4. Identification of a promiscuous epitope in Pfg27 could play a significant role in the design of a subunit vaccine for suppressing malaria transmission.

HLA expression on immature and mature human germ cells

Human leukocyte antigens (HLA) are membrane-bound glycoproteins encoded by the human major histocompatibility complex located on chromosome 6. They are known to function in immnunologic recognition and, with regard to reproduction, a number of non-immune functions have been proposed. Although the expression patterns of the major histocompatibility antigens have been extensively studied at the maternal fetal interface, there are still controversial reports on the expression of these molecules by human gametes and preimplantation stages. This brief review focuses on recent studies where the expression and distribution of HLA on human spermatogenic cells (spermatogonia, primary and secondary spermatocytes, spermatids, spermatozoa), primary and secondary oocytes, and preimplantation embryos have been investigated. These results, and their possible implications for the fertilization process and further embryonic development, will be presented.

HLA-DR is strongly associated with Vogt-Koyanagi-Harada disease in Mexican Mestizo patients

PURPOSE

To analyze the genetic background of human leukocyte antigens (HLA) of Vogt-Koyanagi-Harada (VKH) disease in Mexican Mestizo patients in order to establish whether the pathogenesis is related to the same genes or sequences described in other populations.

PATIENTS AND METHODS

In 48 VKH patients, we performed HLA class I and class II typing using the standard microlymphocytotoxicity tests; a group of 100 nonrelated healthy subjects were analyzed for comparison. Antigen and gene frequencies were calculated for every antigen tested in patients and in controls.

RESULTS

The frequency of HLA-DR4 was significantly increased in VKH Mexican patients (x2Y = 19.95; p = 0.00001; pc = 0.0002; RR = 5.3; EF = 0.52); a discrete increase in DR1 was also found (p = 0.02). HLA-DQ8 also showed a significant association with the disease with a lower RR (3.2) and EF (0.41) than DR4.

CONCLUSION

The strong association found with HLA-DR4 and the slight DR1 increase shown in Mexican patients with VKH suggest that a common shared sequence present in the third hypervariable region of DRB1 genes is relevant for the expression of the disease. The stronger association with DR4 than the one with DQ8 suggests that the DR locus carries the primary susceptibility genes involved in the pathogenesis of VKH.

Absence of linkage between MHC and a gene involved in susceptibility to human schistosomiasis

Six hundred million people are at risk of infection by Schistosoma mansoni. MHC haplotypes have been reported to segregate with susceptibility to schistosomiasis in murine models. In humans, a major gene related to susceptibility/resistance to infection by S. mansoni (SM1) and displaying the mean fecal egg count as phenotype was detected by segregation analysis. This gene displayed a codominant mode of inheritance with an estimated frequency of 0.20-0.25 for the deleterious allele and accounted for more than 50% of the variance of infection levels. To determine if the SM1 gene segregates with the human MHC chromosomal region, we performed a linkage study by the lod score method. We typed for HLA-A, B, C, DR and DQ antigens in 11 informative families from an endemic area for schistosomiasis in Bahia, Brazil, by the microlymphocytotoxicity technique. HLA-DR typing by the polymerase chain reaction with sequence-specific primers (PCR-SSP) and HLA-DQ were confirmed by PCR-sequence-specific oligonucleotide probes (PCR-SSOP). The lod scores for the different theta values obtained clearly indicate that there is no physical linkage between HLA and SM1 genes. Thus, susceptibility or resistance to schistosomiasis, as defined by mean fecal egg count, is not primarily dependent on the host's HLA profile. However, if the HLA molecule plays an important role in specific immune responses to S. mansoni, this may involve the development of the different clinical aspects of the disease such as granuloma formation and development of hepatosplenomegaly.

HLA allele distribution distinguishes sporadic inclusion body myositis from hereditary inclusion body myopathies

We studied the HLA class II associations in patients with sporadic inclusion body myositis (s-IBM) and hereditary inclusion body myopathies (h-IBM) and attempted to distinguish these myopathies on the basis of HLA allele assignments. Forty-five patients, 30 with s-IBM and 15 with h-IBM, underwent HLA class II allele-specific typing using polymerase chain reaction sequence-specific primers for 71 alleles contained in the DRbeta1, DRbeta3-5, and DQbeta1 loci. In s-IBM, we found a high (up to 77%) frequency of DRbeta1*0301, DRbeta3*0101 (or DRbeta3*0202) and DQbeta1*0201 alleles. No significant association with alleles in the DR and DQ haplotypes was found among the 15 h-IBM patients. The strong association of prominent alleles with s-IBM, but not h-IBM, suggests that s-IBM is a distinct disorder with an immunogenetic background that differs from h-IBM.

Several Common HLA-DR Types Share Largely Overlapping Peptide Binding Repertoires

The peptide binding specificities of HLA-DRB1*0401, DRB1*0101, and DRB1*0701 have been analyzed by the use of large collections of synthetic peptides corresponding to naturally occurring sequences. The results demonstrated that nearly all peptides binding to these DR molecules bear a motif characterized by a large aromatic or hydrophobic residue in position 1 (Y, F, W, L, I, V, M) and a small, noncharged residue in position 6 (S, T, C, A, P, V, I, L, M). In addition, allele-specific secondary effects and secondary anchors were defined, and these parameters were utilized to derive allele-specific motifs and algorithms. By the combined use of such algorithms, peptides capable of degenerate DRB1*0101, DRB1*0401, and DRB1*0701 binding were identified. Additional experiments utilizing a panel of quantitative assays specific for nine additional common DR molecules identified a large set of DR molecules, which includes at least the DRB1*0101, DRB1*0401, DRB1*0701, DRB5*0101, DRB1*1501, DRB1*0901, and DRB1*1302 allelic products, characterized by overlapping peptide-binding repertoires. These results have implications for understanding the molecular interactions involved in peptide-DR binding, as well as the genetic and structural basis of MHC polymorphism. These results also have potential practical implications for the development of epitope-based prophylactic and therapeutic vaccines.

Genetic influences on sarcoidosis

To investigate the genetic influences underlying the development of sarcoidosis, HLA class II genotyping was performed in Japanese patients with sarcoidosis and healthy controls using the PCR-RFLP method. The frequencies of both DR52 group antigen-associated alleles (HLA-DRB1*11, -DRB1*12 and -DRB1*14) and DRB1*08 alleles were higher in the patient group, suggesting that the common, specific amino acid residue on the DRB1 molecule of these alleles may determine susceptibility to sarcoidosis. Alternatively, it is possible that another susceptibility gene, linked to these DRB1 alleles, exists within the MHC region. We screened the TNFA, TNFB, HSP70-1 and Hum70t genes around the class III region, as well as the HLA-DMA and -DMB genes in the class II region, for genetic polymorphism in sarcoidosis. None of these genes suggested a susceptibility to sarcoidosis. These studies support the thesis that one of the major genetic factors controlling the development of sarcoidosis is located within the DRB1 locus in the HLA class II region.

MHCPEP, a database of MHC-binding peptides: update 1997

MHCPEP (http://wehih.wehi.edu.au/mhcpep/) is a curated database comprising over 13 000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and where available, experimental method, observed activity, binding affinity, source protein and anchor positions, as well as publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW or FTP.

A three-step allele-level DRB1-DRB3-DRB4-DRB5 genotyping assay using polymerase chain reaction with immobilized sequence-specific oligoprobes

A three-step reverse hybridization assay for allele level-resolution DRB1-DRB3-DRB4-DRB5 genotyping is described. Samples are initially amplified using a generic primer pair for all DRB1-DRB3-DRB4-DRB5 alleles and PCR products are hybridized to generic typing membranes. An intermediate-resolution level genotyping is obtained at this point. Depending on the phenotype, samples are then subjected to a DR1, DR2, DR4, DR52A, DRB3 and/or DRB5 type-specific amplification and hybridization. A third step, involving sequence-specific PCR followed by type-specific hybridization, is only performed to solve certain DR4 and DR52A heterozygous combinations. The assay allows 100% allele level-resolution DRB genotyping. Hybridization membranes contain panels of SSO probes that were optimized to all react specifically under identical stringency conditions. A computer program was written to assist in analysis of the hybridization patterns. The assay was throughly evaluated and has been used to type over 10,000 donors from the Canadian Unrelated Bone Marrow Donor Registry (UBMDR) at allele level-resolution. This method proved to be flexible, easy to update for newly described alleles, easy to perform, fast, and safe. It is also reliable and specific, as 9 novel DRB alleles so far have been detected as aberrant hybridization patterns.

Absolute linkage of celiac disease and dermatitis herpetiformis to HLA-DQ

This report shows the absolute genetic linkage of celiac disease (CD) to the HLA-DQ region, and supports the fact that dermatitis herpetiformis (DH) follows the same pattern of HLA-mediated susceptibility in extensive series of Caucasian Spanish patients. Ninety-five percent of CD (201 of 212) and 100% of DH (55) patients could produce DQ alpha 1*0501-DQ beta 1*02 heterodimers. Negative CD patients for this combination were mostly DR4-DQ8 (DQA1*03-DQB1*0302) (9 OF 11), along with a restricted number of complementary chromosomes. Comparison of observed and expected DQA1-DQB1 genotype distributions (Hardy-Weinberg equilibrium) showed that the excess of patients with DQB1*02 in double doses would be the consequence for which this allele should be complemented by DQA1*0501. Homozygosity for DQA1*0501 would restrain susceptibility to CD and DH.

Polymorphism of the HLA-DMA and DMB genes in rheumatoid arthritis

OBJECTIVE

To determine whether the HLA-DMA and DMB genes, whose encoded molecules are involved in HLA class II-restricted antigen presentation, contribute to the genetic susceptibility to rheumatoid arthritis (RA).

METHODS

One hundred ninety-one RA patients, 147 control subjects, and 218 HLA-DRB1 genotype-matched control subjects were oligotyped for DMA and DMB genes.

RESULTS

DMA*0103 and DMB*0104 were significantly increased in the RA patients compared with the randomly selected and the matched controls, thus indicating a direct influence of the DM genes. After stratification of the patients and matched controls according to DRB1 genotypes, only DMA*0103 was increased in the RA patients with DRB1*01, as well as in the patients negative for the RA-susceptibility DR alleles.

CONCLUSION

Our results suggest that DMA*0103 could play an additional role in the genetic susceptibility to RA.

HLA-DQA1 genotyping by bi-directional sequencing of PCR-amplified DNA spanning exon 2

We describe a simple, reliable technique for HLA-DQA1 genotyping based on direct DNA sequencing of PCR amplified fragments from genomic DNA. The alleles of DQA1 can be divided into two subsets, with one subset demonstrating a 3 base deletion in exon 2 relative to the other. Typing heterozygous individuals who possess one allele from each sub-group can be difficult using a direct sequencing approach, since the two overlapping DNA sequences move out of phase by 3 nucleotides once the point of deletion is reached. The complete sequence is obtained by performing two separate sequencing reactions with fluorescent dye primers, coming from either end of the template. This allows all heterozygous positions in exon 2 to be unambiguously assigned.

Nested polymerase chain reaction-based HLA class II typing for the unique identification of formalin-fixed and paraffin-embedded tissue

Human leukocyte antigen (HLA) genotyping is routinely performed prior to organ transplantation using peripheral blood leukocyte-derived DNA. In addition, polymerase chain reaction (PCR)-based methods have permitted HLA genotyping using DNA extracted from formalin-fixed and paraffin-embedded tissue, with proven applications in HLA-disease association studies and surgical biopsy identification. The utility of current techniques may be limited by the poor yield of intact DNA from such paraffin biopsies. This paper describes a new nested PCR-based HLA class II genotyping method which reliably detects HLA DRB alleles within DNA extracted from even extremely small paraffin biopsies. This method comprises initial PCR amplification of exon II sequences of the HLA DRB1, 3, 4, and 5 genes using generic PCR primers. Identification of the HLA DRB1 alleles and detection of the DRB3, 4, and 5 genes is then performed using a series of separate individual second-round PCR reactions, each of which contains PCR primer pairs detecting a single HLA DRB allele or group of alleles (PCR-SSP). The ability of this method to detect 19 individual HLA DRB1 alleles or groups of alleles, covering all common DRB1 specificities, was confirmed via concordant results when compared with 'direct' (single amplification step) PCR-SSP analysis of one cell line-derived and nine peripheral blood-derived DNA samples, and with five DNA samples extracted from paraffin biopsies. The technique was then successfully applied to 11 further paraffin biopsy-derived DNA samples, of which ten were untypable by 'direct' PCR-SSP analysis, from five cases in which doubt existed as to the individual origin of the tissues.

MHCPEP, a database of MHC-binding peptides: update 1996

MHCPEP is a curated database comprising over 9000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains the peptide sequence, its MHC specificity and, when available, experimental method, observed activity, binding affinity, source protein, anchor positions and publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using WWW, FTP or Gopher.

An unusual DRB1*1503 haplotype without a detectable DRB5 locus in a black African family

A DRB1*1503 allele not associated with DRB5 locus has been detected in an African family during routine HLA typing for bone marrow transplantation. PCR/SSOP analysis showed the DR2-associated alleles in all the family members but the DRB5 locus appeared to be absent in the patient and his brother. The samples were then analyzed for the presence of DRB6 pseudogenes and we found that the unusual haplotype was associated with DRB6*0101 allele. This finding strengthen the hypothesis of a recombination hot spot between DRB1 and DRB6 genes.

HLA-A*02 subtype distribution in Caucasians from northern Italy: identification of A*0220

This study describes a comprehensive easy to perform PCR-SSOP typing approach suitable for complete genomic subtyping of HLA-A*02. A single 1.6 kb PCR-amplificate spanning exons 2, 3 and 4 of the HLA-A*02 gene was used for hybridization with a panel of twenty-four SSOPs. This allowed unequivocal assignment of all so far known HLA-A2 subtypes, including A*0209 and A*0215N which differ for nucleotide substitutions in exon 4, without the need for two separate amplifications. Using this approach, HLA-A*02 subtype distribution was analyzed in 218 samples from unrelated, healthy individuals from northern Italy enrolled in the Italian Bone Marrow Registry and typed as HLA-A2 by serology or generic molecular analysis. As expected, A*0201 was found in the majority (92.6%) of samples. However, a significant number (6.8%) of individuals carried A*0205. Furthermore, A*0202, A*0208, A*0209 and A*0217, so far not described in Caucasians, were detected in a low number of samples (frequency ranging from 0.45% to 1.8%). Finally, a novel HLA-A*02 subtype, A*0220, was detected in 0.9% of the samples. As confirmed by DNA sequencing of exons 2 and 3, this allele is identical to A*0201 except for a single nucleotide substitution in codon 66 which changes the predicted amino acid sequence form Lys to Asn. The findings of this study have implications for the selection of HLA-A*02+ donors in unrelated bone marrow transplantation and of patients for specific immuno-therapy with HLA-A*02 restricted peptide vaccines.

HLA-C genotyping of patient with Behçet's disease in the Japanese population

Behçet's disease has been known to be strongly associated with a particular HLA-B allele, B51. To address the possibility that the HLA-C gene, which is closely linked to HLA-B but has been poorly defined for allo-antigen specificity by the serologic method is involved in the susceptibility to Behçet's disease, HLA-C genotyping was performed for 90 Japanese Behçet's disease patients by the PCR-SSP method. The frequencies of HLA-Cw*14 and -Cw*15 were significantly higher in the patient with Behçet's disease as compared to the controls (48.9% vs. 24.0%, p = 0.0005, and 17.8% vs. 7.3%, p = 0.0434, respectively). On the other hand, the frequencies of HLA-Cw*0304 and -Cw*01 were significantly decreased in the patient group as compared to the control group (7.8% vs. 25.0%, p = 0.0027, and 23.3% vs. 37.5%, p = 0.0398, respectively). The significantly higher HLA-Cw*14 and -Cw*15 alleles may tightly correlate with the B51 antigen, and hence may have increased as a result of a linkage disequilibrium with B51. Accordingly, the HLA-C allele frequencies were compared for the B51-positive or -negative patients and controls, but there was no HLA-C allele showing a significant difference between these patient and control groups. Conversely, analysis of the HLA-B allelic distribution in association with HLA-Cw*14 revealed that in the healthy controls, B44 and B51 were present at the frequencies of 57.1% and 35.7% of the HLC-Cw*14-positive individuals, respectively. In contrast, in the Cw*14-positive patients the frequency of B44 was merely 14.0% (p = 0.0001) and that of B51 was significantly high, amounting to 82.0% (p = 0.0001). These facts suggest that the pathogenic gene of Behçet's disease is not the HLA-C gene (HLA-Cw*14 and/or HLA-Cw*15) but the HLA-B gene (HLA-B51) itself or a non-HLA gene residing in the centromeric side of the HLA-B gene rather than in the telomeric side around the HLA-C gene. This finding supports our previous mapping result, which located the susceptible gene between the TNF and HLA-B genes.

Immunodominance of seven regions of a major allergen, Cry j 2, of Japanese cedar pollen for T-cell immunity

The immunodominant regions of the Japanese cedar pollen allergen Cry j 2 for T-cell immunity were determined with whole peripheral blood lymphocytes (PBL) derived from seven allergic patients and three nonallergic subjects. Cry j 2-stimulated T-cell proliferation was inhibited by anti-HLA-DR, but not by anti-HLA-DQ antibody, indicating that the responding T cells recognized the allergen peptides associated with HLA-DR molecules. It was found that seven regions of Cry j 2, i.e., regions corresponding to amino acid numbers 1-26, 70-84, 151-167, 187-203, 252-279, 283-314, and 345-362, were immunodominant for T-cell proliferation. Thus, Cry j 2 bears a limited number of immunodominant regions despite polymorphic features of HLA-DR in the immune system. This suggests the possibility of molecularly designing Cry j 2 antagonists that could downregulate allergic reactions to Japanese cedar pollen.

High frequency of HLA-A*0207 subtype in Chinese population

BACKGROUND

HLA-A2 is the most polymorphic and most common HLA phenotype found in various ethnic populations. Seventeen HLA-A2 subtypes have been reported and characterized by molecular techniques. Differences among these subtypes are limited to a few amino acids. Among them, HLA-A*0201 is the predominant subtype among whites. The results of a recent study, however, suggest that the HLA-A*0207 subtype may be present at a high frequency in the Chinese population.

STUDY DESIGN AND METHODS

To determine the exact frequency of the HLA-A*0207 subtype in the Chinese population, genomic DNA samples obtained from 54 HLA-A2-positive Chinese in Taiwan were studied by using sequence-specific primers and polymerase chain reaction.

RESULTS

HLA-A*0207 was present in 56 percent of the studied subjects. The estimated gene frequency for HLA-A*0207 is 17.8 percent in the Chinese population.

CONCLUSION

HLA-A*0207 is the most common HLA-A2 subtype among Chinese. The high frequency of the HLA-A*0207 allele in this population offers a unique opportunity to study the ways in which different HLA-A2 subtypes may influence the clinical outcome of allograft transplantation and the disease susceptibility of recipients.

Results of Expedicion Humana. II. Analysis of HLA class II alleles in three African American populations from Colombia using the PCR/SSOP: identification of a novel DQB1*02 (*0203) allele

PCR/SSOP typing methods were used to analyze the HLA Class II DRB1, DQA1, DQB1 and DPB1 loci of samples from three African American populations of Colombia. Forty samples from the Cauca (Pacific), and twenty samples each from the Choco (North Pacific Coast) and the Providencia (Caribbean island) populations, were collected and the Class II loci analyzed under the auspices of the Expedicion Humana. Despite the limited number of samples analyzed, the African Colombian populations exhibit a very high degree of class II polymorphism. A great diversity of DRB1 alleles was found, with representatives from all serological classes, including 19 DRB1 alleles in the Providencia, 16 in the Cauca and 14 in the Choco groups. In addition, a novel DQB1*02 allele (*0203) was found in two individuals from the Cauca population of the Pacific Coast. The sequence of the DQB1*0203 allele, associated with DR3, differs from DQB1*0201 by only one nucleotide substitution (C-->A) in the second position of codon 57, resulting in an Ala to Asp change. The addition of DQB1*0203 brings the total number of DQB1 alleles identified to date to 26. HLA class II diversity is much greater in these African Colombian populations than that seen in nearby Amerindian populations. Analysis of regional Colombian African American HLA population genetics is discussed with respect to the Colombian Amerindian HLA genetics described in an accompanying paper.

Direct role of HLA-B5 in influencing susceptibility to Takayasu aortoarteritis

To investigate genetic factors involved in the pathogenesis of Takayasu arteritis (TA), North Indian patients belonging to the states of Punjab, Haryana, Uttar Pradesh and Delhi were examined for HLA-class I and class II antigens and the data compared with healthy controls from the same ethnic group. Additionally, DNA typing was performed using polymerase chain reaction/sequence specific oligonucleotide probe (PCR-SSOP) technique to evaluate the distribution of molecular alleles in the healthy Indian population as compared to orientals and Western caucasoids. The frequency of HLA-B5 was significantly increased in patients as compared to controls (chi 2 = 32.5, corrected P value, Pc = 3 x 10(-6), relative risk = 4.3). Serological splitting of B5 into B51 and B52 did not reveal an association with any of the two subtypes. Weak association was also noticed with DR8 in the patient group (chi 2 = 8.2, Pc = 0.05). Distribution of the molecular subtypes of various HLA-B and DR alleles indicated that although the Indian population is essentially caucasoid, it comprises of an admixture of both caucasoid as well as oriental alleles/haplotypes. The observations clearly suggest that (a) HLA-linked genes are involved in the development of Takayasu arteritis, and (b) rather than a subtype of B5, the whole molecule or its closely linked gene(s) influence susceptibility to TA.

The HLA system: an update and relevance to patient-donor matching strategies in clinical transplantation

In recent years the development of recombinant DNA and sequencing techniques has led to a greatly increased understanding of the genetic complexity, structure and function of the human major histocompatibility complex. This system may be subdivided into the "classical' HLA (human leukocyte antigen) class I and II transplantation antigens and novel HLA and non-HLA genes, involved in antigen processing and presentation to T cells. Parallel technological developments in HLA DNA typing in the clinical laboratory have resulted in a more precise awareness of the role of HLA matching for the classical HLA antigens in bone marrow and solid organ transplantation, while alternative strategies and techniques for donor selection are currently under evaluation. This review offers a current perspective on the genetics, structure and function of the HLA system, its relevance to clinical transplantation and future prospects for improvements in donor selection.

DNA-based HLA typing for cord blood stem cell transplantation

Molecular analysis of the HLA loci has revealed a pattern of extensive sequence polymorphism. For the class II loci, the polymorphism is localized to the second exon, whereas for the class I loci, both the second and third exons are polymorphic. These polymorphic regions encode the peptide binding groove and appear to be functionally significant in terms of disease susceptibility and transplantation. However, much of this polymorphism cannot be detected by serologic HLA typing methods. DNA typing methods based on PCR amplification and hybridization with sequence-specific oligonucleotide (SSO) probes can distinguish the many allelic sequence variants identified at these loci. The use of arrays of immobilized SSO probes allows genetic typing at many polymorphic sequence motifs in a single PCR and single hybridization reaction, making possible the development of simple, robust, and automated tests. PCR-SSO probe typing of the HLA loci requires very little sample material, is capable of either general or fine discrimination of alleles, and can be used to detect maternal contamination of cord blood. The application of this approach to typing HLA class I and II loci is discussed with regard to hematopoietic transplantation therapy.

Analysis on allelic variation of the HLA-DMB gene in Japanese by PCR-RFLP as well as direct DNA sequencing and identification of a new DMB allele, DMB*0105

In the HLA-D region, one of the class II genes, DMA and DMB have been identified between the DQ and DP genes, and four allelic polymorphisms in each of the DMA (DMA*0101 approximately 0104) and DMB (DMB*0101 approximately 0104) genes have been so far recognized. Several recent studies suggested that the DM molecule is required for class II antigen presentation pathway especially by promoting the binding of antigenic peptides to the classical HLA class II molecule. In this study, we have analyzed genetic polymorphism and allelic variation of the DMB gene in a Japanese population by the direct DNA sequencing technique and also by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, and could recognize DMB*0101 (49.3%), DMB*0102 (23.2%), DMB*0103 (23.2%), and DMB*0104 (0.4%). Further, a new DMB allele, DMB*0105 characterized by the presence of Val and Ile at two polymorphic sites, codons 144 and 179, respectively was identified. Strong linkage disequilibria were found between DMB*0101 and DRB1*0101, DPB1*0402 and DRB1*1502, and also between DMB*0103 and DRB1*1501 and DQB1*0602. HLA-DMB genotyping using the PCR-RFLP method established here will provide accurate evaluation of the effects of sequence allelism in the DMB gene on the HLA class II disease associations.

Further molecular diversity in the HLA-B15 group

In order to further clarify the diversity of the HLA-B15 antigens and the correspondence of serological types with alleles in Asians, we screened various B15 serological splits by means of a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method. Subsequently, the genes encoding various B15 variants were sequenced. Two novel alleles, B*1528 and B*1529, were identified: the nucleotide sequence of the former contained a single-base substitution at position 263 in exon 2 as compared to that of the B*1501 allele, which results in an amino acid change at position 64 in the alpha 1 domain, and the nucleotide sequence of the latter differs from that of B*1518 by a single-base substitution at position 272 of exon 2 which results in an amino acid change at position 67 of the alpha 1 domain. One new allele, B*1521, described recently in Australian Aborigines was also identified in Asians in the present study. Moreover, the results of sequencing demonstrated that Asian HLA-B62, B70, and B77 antigens are encoded by B*1501, B*1518, and B*1513, respectively. Two splits of B75 antigens, B75V (TS-1) and B15N, which have been proposed to exist in the Japanese population were encoded by B*1511 and B*1502, respectively. Most of the B15 alleles detected in the present study showed positive associations with other locus antigens. Especially, B*1502 was strongly associated with Cw8, while B*1521 was strongly associated with A34 and Cw6.

Definition of an HLA-A3-like supermotif demonstrates the overlapping peptide-binding repertoires of common HLA molecules

An HLA-A3-like supertype (minimally comprised of products from the HLA class I alleles A3, A11, A31, A*3301, and A*6801) has been defined on the basis of (a) structural similarities in the antigen-binding groove, (b) shared main anchor peptide-binding motifs, (c) the identification of peptides cross-reacting with most or all of these molecules, and (d) the definition of an A3-like supermotif that efficiently predicts highly cross-reactive peptides. Detailed secondary anchor maps for A3, A11, A31, A*3301, and A*6801 are also described. The biologic relevance of the A3-like supertype is indicated by the fact that high frequencies of the A3-like supertype alleles are conserved in all major ethnic groups. Because A3-like supertype alleles are found in most major HLA evolutionary lineages, possibly a reflection of common ancestry, the A3-like supermotif might in fact represent a primeval human HLA class I peptide-binding specificity. It is also possible that these phenomena might be related to optimal exploitation of the peptide specificity by human TAP molecules. The grouping of HLA alleles into supertypes on the basis of their overlapping peptide-binding repertoires represents an alternative to serologic or phylogenetic classification.

PCR-LIS-SSCP (Low ionic strength single-stranded conformation polymorphism)--a simple method for high-resolution allele typing of HLA-DRB1, -DQB1, and -DPB1

We have developed a simple and efficient procedure with which to form single-stranded DNA [ssDNA] and then applied HLA-DRB1, -DQB1, and -DPB1 allele typing. This method is referred to as low ionic strength single-stranded conformation polymorphism (LIS-SSCP), and is based on the diversity in the electrophoretic mobility of ssDNA formed by heat denaturation in low ionic strength solutions. This method detected DNA polymorphisms, including point mutations at a variety of positions in the DNA fragments of the HLA-DRB1, -DQB1, and -DPB1 genes. Under our experimental conditions, stable ssDNA could be kept at room temperature > or = 5 hr without having been cooled on ice immediately after heat denaturation. A total of 41 HLA-DRB1, 14 HLA-DQB1, and 17 HLA-DPB1 alleles from 220 healthy people were analyzed using a combination of PCR-LIS-SSCP with group-specific amplification. All of the alleles analyzed were discriminated among the DRB1, DQB1, and DPB1 groups except for DPB1*0402 and 0201. The efficiency of ssDNA formation using the LIS-SSCP procedure was higher than that of the traditional formamide method, and the SSCP profiles were clearer than those of the original SSCP. This procedure is useful for screening new alleles as well as the donor-recipient molecular matching of HLA class II genes. It is simple, rapid, and cost effective, requiring neither radioisotopes nor enzymes to confirm the typing results of other methods.

Seronegative spondyloarthropathies and HLA-B27 subtyes: a study in Asian Indians

In this study, 60 HLA-B27+ve SSA patients and 17 healthy controls belonging to North India were analyzed to ascertain heterogeneity of the B27 molecule in this population. ID-IEF and PCR-SSOP technologies were used to analyze polymorphism in exon 2 and 3 of the HLA-B27 gene. Four different subtypes were encountered: B*2702,04,05 and 07. Other subtypes of B27 viz B*2701,03,06 and 08 were not encountered. B*2704 (common oriental subtype) and B*2705 (common Caucasian subtype) were the most common subtypes in the control and patient groups. B*2707 was less frequently encountered in both groups and B*2702 was found in only one AAU patient. B*2704 was the predominant subtype in the AS group (70.8%) compared to its frequency of 47% in healthy controls (RR = 2.73) while in the undiff SpA group, B*2705 occurred most frequently (73.1%, RR = 3.05). B27 subtypes segregated differently in males and females. 12 of the 17 male AS patients carried B*2704 as compared to 1 of 8 healthy males (X2 = 3.9, P < 0.05). On the other hand, in the undiff SpA, B*2705 was significantly raised in female patients (100%) as compared to healthy females (22.2%, X2 = 4.9, P < 0.05). Subtype distribution is indicative of racial admixture in the Asian Indian population.

MHCPEP--a database of MHC-binding peptides: update 1995

MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding affinity, source protein, anchor positions, as well as publication references. The present format of the database allows text string matching searches but can easily be converted for use in conjunction with sequence analysis packages. The database can be accessed via Internet using Gopher, FTP or WWW.

Polymorphism in both X and Y box motifs controls level of expression of HLA-DRB1 genes

The HLA class II antigens of the human major histocompatibility complex play an important role in immune response. The quality of the immune response is determined not only by polymorphisms in their coding region, but also by the level of their cell-surface expression which affects, for example, the extent of T-cell activation. We have previously described allelic polymorphisms in the upstream regulatory regions of HLA-DRB genes, which affected DNA-protein interactions and resulted in significantly different promoter strengths. In the present study, we investigated the effect of polymorphisms in the X and Y box motifs on the transcriptional activity of DRB1 gene promoters in the DR1, DR51, and DR53 haplotype groups. We used normal, chimeric, and mutated DRB promoters and compared their relative abilities to initiate transcription of the CAT reporter gene in human B-cell lines. The results show that polymorphisms in both the X1 and Y box motifs play a dominant role in the promoter strength. In the gel mobility shift assay, we observed differential ability of nuclear proteins that bind to the polymorphic X1 and Y box elements. The results in the present study confirm earlier data in that the nucleotide variation in the X1 box affects the level of expression of DRB1 genes. In addition, the present data demonstrate that polymorphism in the Y box, which affects the inverted CCAAT sequence, also plays a dominant role in the transcriptional activity of DRB1 promoters.