Complementarity and redundancy of the binding specificity of HLA-DRB1, -DRB3, -DRB4 and -DRB5 molecules

The second HLA-DR molecules, which are encoded by loci different from HLA-DRB1 are weakly polymorphic. Predominant alleles such as HLA-DRB3*0101, HLA-DRB4*0101 and HLA-DRB5*0101 are therefore interesting targets to define antigenic peptides with major impact for the entire population. Strikingly, they have been poorly investigated. Thus we have characterized peptides from the major bee venom allergen that bind efficiently to these molecules and compared them to peptides specific for preponderant HLA-DRB1 molecules. Interestingly, DRB5*0101 and DRB1*0701 molecules share four binding peptides and use some identical anchor residues. Similarities are also found between DRB3*0101 and its haplotype-associated molecules DRB1*0301 and DRB1*1301. In sharp contrast, DRB4*0101 exhibits a unique binding specificity, which results from particular structural features of its peptide binding site. Ybeta81 seems to alter the amino acid preferences of the P1 pocket, while Rbeta71, Ebeta74, Nbeta26 and Cbeta13 confer to the P4 pocket a unique topology. Our results show that the two HLA-DR molecules expressed in most haplotypes studied here have mostly complementary binding patterns. Only haplotype HLA-DR52 exhibits peptide binding redundancies. Finally our results document functional similarities among HLA-DR molecules and allow us to propose peptide sequences that might be useful for bee venom immunotherapy.

Quantitative calculations of antibody--antigen binding: steroid--DB3 binding energies by the linear interaction energy method

Linear interaction energy/molecular dynamics calculations have been used to compute steroid/antibody binding energies. The absolute binding affinities of 10 steroids to antibody DB3 and of a hapten to catalytic antibody 1E9 are computed and compared to experiment. A detailed analysis of the molecular origins of the observed binding patterns is provided. The binding energy of an untested steroid is predicted.

Identification of three new DRB3* (DRB3*0106, DRB3*0107 and DRB3*02022) alleles

Three novel DRB3* alleles were identified using CANTYPE reverse hybridization assay. The initial unusual hybridization patterns of DRB3-specific polymerase chain reaction (PCR)-amplified DNA from each subject were confirmed by cloning and sequencing analysis. DRB3*0106 allele is identical to DRB3*0101 except for a single nucleotide substitution (CTG-->GTG) changing codon 38 from Leu to Val. This polymorphism is commonly found in DRB3*03 alleles. Compared with DRB3*0202, DRB3*02022 contains a single silent nucleotide substitution (AAT-->AAC, both encoding for Asn) at codon 77. This polymorphism is also present in DRB3*0204 allele. The new DRB3*0107 allele has a sequence unique to DRB3 alleles. From codon 5 to codon 36 the sequence is identical to that of DRB3*0101 allele. From codon 37 to codon 87 the sequence of DRB1*0107 allele is identical to that of DRB3*0202. This sequence would thus explain the CANTYPE(R) DRB3-specific unusual pattern of reactions. The new DRB3*0107 could have arisen from a gene conversion between DRB3*0101 and DRB3*0202 alleles, but the DRB3*0106 and the DRB3*02022 may have been generated by a point mutation event. The DRB3*0107 allele was identified in a Caucasoid individual. The ethnic origin of the subjects carrying the other two alleles are unknown. The three alleles presented here were only identified once, in a total population of 49,000.

Analysis of HLA haplotypes in autoimmune hepatitis type 1: identifying the major susceptibility locus

Susceptibility to autoimmune hepatitis type I (AIH-1) has been associated with HLA-DR3, DR52, and DR4 antigens in Caucasian and Oriental patients. However, in Brazil, disease susceptibility is primarily linked to DR13 and DR52. In this highly admixed population, we find different DR13-associated haplotypes, presenting a unique opportunity to discriminate relevant genes within a tightly linked genomic region. To identify the primary susceptibility locus, we sequenced DR13 alleles of 39 patients with AIH-1 and 22 controls. Patients were almost exclusively DRB1*1301, but half of controls typed DRB1*1302. HLA-DQ haplotypes were varied. Oligotyping of DRB3 locus of all patients and also within the HLA-DR13 positive group showed an allele distribution comparable to controls, confirming that the stronger association lies in the DRB1 locus. On the other hand, if DRB1*1301 is the major susceptibility factor in our sample, the only amino acid different from DRB1*1302 in position 86, corresponding to pocket 1 in the peptide-presenting groove, may be important. We propose that peptide presentation leading to pathogenesis of AIH-1 may be quite stringent, but will also be affected by other strong genetic or environmental susceptibility factors, which would explain the various HLA molecules associated to the disease in the different populations.

HLA-DRB1*03, DRB1*11 or DRB1*12 and their respective DRB3 specificities in clinical variants of sarcoidosis

Determination of DRB1 and DRB3 specificities in sarcoidosis patients identified that the presence of DRB1*03 and the absence of DRB1*11 and/or DRB1*12 favors a course of disease that is associated positively with Löfgren's syndrome (DRB1*03) and negatively with stage I disease (DRB1*11 and/or 12). In common with normal controls, DRB1*03 was associated with DRB3*0101 and DRB1*11/12 with DRB3*0201/2. An analysis of DRB1 and DRB3 associations in variants of sarcoidosis revealed that DRB1*03 and DRB3*0101 were associated with Löfgren's syndrome in a combined association fashion. Conversely, a lack of DRB1*11 and/or DRB1*12 but not DRB3*0201/2 favored the clinical course of sarcoidosis.

Association of bovine DRB3 alleles with immune response to FMDV peptides and protection against viral challenge

We have analysed the influence of bovine MHC (BoLA) polymorphism on the immune response and degree of protection induced by peptide vaccines against foot-and-mouth disease (FMD) in cattle. The peptides used for animal immunisation were: A (VP1(138-156)), AT (peptide A linked to VP1(21-40)) and ACT (peptide A, linked to VP1(196-209) and VP1(21-40)). Sixteen different DRB3 types were found among the 46 cattle analysed by PCR-RFLP typing. No absolute correlation was observed, for any type, with the serum neutralising titres (SNT) values and the protection induced. However, among the most common haplotypes present, associations were observed between expression of different types with the levels of SNT and/or protection induced by peptides A and ACT. Thus, types DRB3.2*1, 3 and 7 were associated with increased levels of protection. In contrast, types DRB3.2*12 and 18 were associated non-protection, and DRB3.2*12 was also associated with low SNT titres. Overall, the results indicate that the polymorphism in BoLA class II molecules affects both the immune response and protection induced by potential FMD peptide vaccines.

Two novel DRB alleles detected by PCR-SSO and confirmed by sequencing: DRB1*0317 and DRB3*0210

We here describe two new DRB alleles (DRB1*0317 and DRB3*0210) which were detected by polymerase chain reaction using sequence-specific oligonucleotides (PCR-SSO) and confirmed by direct sequencing. The exon 2 sequence of DRB1*0317 is the result of an intergenic recombination event yielding a hybrid allele between 5'DRB1 and 3' DRB3 sequences with the recombination breakpoint located between codons 39-51. The new DRB3*0210 allele is closest related to DRB3*02021 except for a single nucleotide position at codon 51. Here, the sequence AGG at codon 51 which was a group-specific motif for all DRB3*02 alleles described previously, is replaced by the DRB consensus sequence ACG.

Severe neonatal alloimmune thrombocytopenia due to anti-HPA-3a

BACKGROUND AND OBJECTIVES

Neonatal alloimmune thrombocytopenia is usually attributable to HPA-la antibodies. We report a case of parental platelet antigen incompatibility associated with a severe neonatal thrombocytopenia secondary to alloimmunization to HPA-3a.

MATERIALS AND METHODS

Platelet antibodies were detected by the monoclonal antibody-specific immobilization of platelet antigens, genotyping of the platelets by PCR, and HLA typing by serologic procedures and PCR.

RESULTS

Genotyping of maternal and paternal platelets confirmed the incompatibility in the HPA-3a system. It is noteworthy that the mother is of the HLA type DRB3*0101, is ABO-incompatible with her husband, and also has HLA class I antibodies.

CONCLUSION

Severe neonatal thrombocytopenia associated with HPA-3a alloimmunization is infrequent and all the factors mentioned above could have played a role in the severity of the disease.

Identification by sequencing based typing and complete coding region analysis of three new HLA class II alleles: DRB3*0210, DRB3*0211 and DQB1*0310

The study of HLA class II polymorphism by direct exon 2 DNA sequencing analysis has been established to be a reliable and accurate high-resolution typing procedure. This approach shows some advantages in relation to previous methods, polymerase chain reaction using sequence-specific oligonucleotides (PCR-SSO) and sequence-specific primers (PCR-SSP), basically due to the capability of analysis for the complete sequenced genomic region, including non-polymorphic motifs. DRB3 and DQB1 sequencing based typing (SBT) in unrelated bone marrow donor searching allowed us to detect three new alleles. The complete coding region sequences were characterised from cDNA. Two new DRB3 alleles, DRB3*0210 and DRB3*0211, were described in two Caucasian bone marrow donors. Both sequences showed single point mutations regarding DRB3*0202, producing amino acid replacements at positions 51 (Asp to Thr) and 67 (Leu to Ile), respectively. These two point mutations can be found in other DRB alleles, and suggest that gene conversion would be involved in the origin of both alleles. A new DQB1 sequence was found in a Spanish patient that showed two nucleotide differences, positions 134 and 141, with regard to its close similar DQB1*03011 allele. Only substitution at position 134 provoked amino acid replacement at residue 45, Glu to Gly. This single amino acid change would be involved in the lack of serologic recognition of this new molecule by DQ7-specific reagents.

HLA-A, -B, -C, -DRB1, DRB3, DRB4, DRB5 and DQB1 polymorphism detected by PCR-SSP in a semi-urban HIV-positive Ugandan population

PCR-SSP was used to HLA-type a cohort of Ugandan HIV-positive individuals. The results represent a more comprehensive description of HLA in an African population than previously described and are in concordance with data from a general Black population. Substantial differences exist between this population and Caucasoid populations in which immunological responses to HIV have been investigated; this emphasises that the main HLA-restrictive elements for HIV-specific cytotoxic T lymphocytes will most likely be different for each population.

Relative frequencies of DRB1*11 alleles and their DRB3 associations in five major population groups in a United States bone marrow registry

One hundred sixty-one individuals from each of five US population groups, Caucasians (CAU), African Americans (AFA), Asians/Pacific Islanders (API), Hispanics (HIS), and Native Americans (NAT), were randomly selected from a volunteer bone marrow registry database consisting of 14,452 HLA-DRB1*11 positive individuals. This sampling provided at least an 80% probability of detecting a rare allele that occurred at 1% in the DRB1*11 positive population. Samples were typed for DRB1*11 alleles by polymerase chain reaction-sequence specific oligonucleotide probe typing (PCR-SSOP). A total of 10 DRB1*11 alleles out of 27 possible alleles were detected. The distribution and diversity of DRB1*11 alleles varied among populations although DRB1*1101 was the predominant DRB1*11 allele in all populations. Caucasians were the least diversified; only four common alleles (DRB1*1101-*1104) were observed. As well as the four common alleles, other groups also carried one or two other less frequent alleles including DRB1*1105 (API), *1106 (API), *1110 (AFA), *1114 (HIS), *1115 (NAT), and *1117 (AFA). A subset (418) of these individuals were also typed for DRB3 alleles. Most (97.6%) showed a strong association of DRB1*11 with DRB3*0202.

Identification of two new alleles HLA-DRB1*0312, DRB1*0432 and of a DRB3-negative DRB1*1313-positive haplotype

Two new HLA-DRB1 alleles were identified in the course of routine class II molecular typing in Dutch Caucasoid. HLA-DRB1*0312 is similar to *03011 except for codon 57 (GAT-->AGC). DRB1*0432 is similar to *0413 but with a mutation at position 215, changing codon 72 (CGG-->CAG; Arg-->Gln). This sequence has never before been identified at this position. A DRB3-negative DRB1*1313 haplotype was identified in an individual from Indonesia. Monoclonal antibodies against DR52 were nonreactive with lymphocytes of this individual. The DRB1*1313-DRB3-negative haplotype probably represents a recombination of DRB1*13 and *08 haplotypes where the sequences telomeric of HV1 are derived from the DRB3-negative DRB1*0803 haplotype.

Identification of a new DRB3*02 allelic variant (DRB3*0209) by high-resolution sequence-based typing

The HLA-DRB3/B4/B5 sequence-based typing method developed in this study in combination with PCR-SSP, enabled us to identify a new DRB3*02 allele, that was named as DRB3*0209 (GenBank accession number AF148518). This name has been officially assigned by the WHO Nomenclature Committee in May 1999. The new allele differs from DRB3*0207 by one substitution in codon 51 from AGG to ACG and another in codon 60 from TAC to TCC, resulting in aminoacid changes from Arg-->Thr (codon 51) and from Tyr-->Ser (codon 60). The DRB3*0209 allele was discovered in two related North Italian families. The fact that it was present in an hemizygous situation in three members of the paternal family and in one member of the secondary related family enabled us to isolate and sequence the new DRB3 allele without cloning, to identify its association with the DRB1 locus, and to generate an Epstein-Barr virus (EBV)-transformed cell line, now present in our ECBR (European Collection for Biomedical Research) Cell Line Bank.

HLA-DRB1,3,4,5 and -DQB1 allele frequencies and HLA-DR/DQ linkage disequilibrium of 231 German caucasoid patients and their corresponding 821 potential unrelated stem cell transplants

Allelic matching within the HLA-DRB1 and -DQB1 loci significantly improves the clinical outcome of hematopoietic stem cell transplantation. Consequently, allelic typing of these loci is strongly recommended for the unrelated stem cell donor selection. In this study, the HLA-DRB1,3,4,5 and -DQB1 alleles of 231 patients and their corresponding 821 nonrandom potential stem cell donors were determined to define compatible donor/recipient pairs. Highly accurate HLA typing data were achieved by PCR-SSOP and a combination of group specific PCR-SSP and subsequent sequencing-based typing of nearly the whole second exon of each locus. The alleles DRB1*07, *09, and *10 were analyzed by PCR-reverse dot blot hybridization instead of sequencing. Additionally, DRB1 homozygosity was verified by temperature gradient gel electrophoresis. The identified 2104 HLA-DRB1 and HLA-DQB1 alleles as well as data on HLA-DRB3, -DRB4, and -DRB5 alleles were applied to a statistical program and absolute and relative delta values of DR/DQ linkages were calculated. The achieved data on the HLA-DRB1 allele distribution and on DR/DQ associations in terms of subtypes significantly ensure the typing reliability, since rare allele combinations will result in further investigations. Furthermore, detailed data on the DR/DQ allele associations allow estimations of the number of HLA-A, -B, and -DR matched unrelated stem cell donors necessary for the identification of DRB and DQB subtype identical donors.

Sequence and transfection of BoLA-DRB3 cDNAs

Bovine MHC (BoLA-) DRB3 alleles encoded by the DH8A, DH22A and DH24A class II haplotypes were cloned from cDNA and characterized by sequence analysis. Comparison with other full-length DRB3 sequences suggested that DRB3 alleles may have evolved through multiple lineages. All three BoLA-DRB3 alleles were shown to express on the surface of transfected cells, and the transfectants were used to define or confirm the class II specificity of a panel of monoclonal antibodies.

DRB3 alleles with variations in the annealing sites of commonly used amplification primers

New HLA alleles are often identified initially from observing uncommon patterns found in low-resolution typing performed via polymerase chain reaction using sequence-specific oligonucleotide probes (PCR-SSOP). Recently, the HLA-DR oligotyping analysis of two Caucasian, one Caucasian/American Indian and two African American individuals resulted in the identification of three novel DRB3 alleles. Using DRB-specific primer sets commonly employed in amplification-based typing, all four individuals were originally characterized as DRB3 negative. Direct sequencing identified DRB3*0104 (variation at codon 8, TCG instead of TTG), and DRB3*0101202 (variation at intron (-13), G instead of C). One individual appeared to carry a DR52-associated DRB1 allele without an associated DRB3 allele. Lack of conservation at the junction of intron 1 and exon 2 of the DRB3 gene suggests that commonly used DRB-specific primer sets may need to be modified.

The human leukocyte antigen HLA DRB3*020/DQA1*0501 haplotype is associated with Graves' disease in African Americans

Information on genetic susceptibility to Graves' disease in African Americans is limited. We studied DRB1, DQB1, DRB3 subtypes, DQA1*0501, DQA1*0201, and CTLA-4 polymorphisms in 49 African American patients with adult onset Graves' disease and 47 racially-matched controls using PCR-based sequence-specific priming methods. There were no significant differences in DRB1 or DQB1 allelic frequencies or CTLA-4 polymorphisms between patients and controls. However, we found that the frequency of DRB3 was significantly increased in the patients (75.5% vs. 57.4%, P = 0.006, X2 = 3.52), especially for the DRB3*0202 subtype (53.1% vs. 23.4, P = 0.003, X2 = 8.91). In this one respect, the finding was in concordance with our previous observations in Caucasian patients with adult-onset Graves' disease. In addition, whereas the frequency of DQA1*0501 was increased (P = 0.018, X2 = 5.63) in our patients, the haplotype of DRB3/DQA1*0501, or DRB3*0202/DQA1*0501 was found to be more strongly associated (P = 0.008, X2 = 7.0; P = 0.0008, X2 = 11.34, respectively). These data suggest that DRB3*0202, particularly when found with DQA1*0501 in a haplotype is a susceptible gene(s) for Graves' disease in adult African Americans. Considering these data with those in Caucasian patients, our results would suggest that the primary Graves susceptible locus is likely DRB3 and not DRB1.

[HLA-DRB alleles polymorphism in Han, Hui, Uygur and Tibetan populations in northwestern China]

According to the 11th THW standard, we designed a pair of primers by which a segment of 256bp of HLA-DRB1, B3, B4, and B5 could be amplified simultaneously. Twenty-seven oligonucleotide probes were designed and synthesized for 39 loci on DRB1, 3 on DRB3, 1 on DRB4 and 3 on DRB5. A PCR-SSO DNA typing protocol was built, which met the standard of HLA class II DNA typing in 11th IHW. With this method, 186 of Chinese (Han) in Xi'an, 169 of Hui in Ningxia, 200 of Uygur in Xinjiang, and 188 of Tibetan in Tibet were detected with a comparison study. The genetic distribution of 46 loci of DRB in four ethnic healthy populations were surveyed. No diversity has been found between Han and Hui in DRB. DRB1 * 02(16.9%), DRB1 * 07 (13.1%), and DRB1 * 09(12.0%) were the higher frequent loci in Han. More DRB loci were detected in Tibetan but without higher loci as in Han and Hui. The DRB polymorphism of Uygur population was similar to Caucasian. A discriminative highest frequency of DRB1 * 07(23.8%) was found in Uygur, which implied a selection happened.

New HLA class II alleles in the Indonesian population

This paper describes two new class II alleles of the major histocompatibility complex (MHC), DRB1*1431 and DRB3*0303, that have been found in the Indonesian population. In addition, the identification of DRB1*0819 is presented as a confirmatory report.

Relative HLA-DRB1*13 allele frequencies and DRB3 associations of unrelated individuals from five US populations

The frequencies of 30 HLA-DRB1*13 alleles and 15 DRB3 alleles were determined for the 5 major U.S. ethnic populations: Caucasians, African Americans, Asian/Pacific Islanders, Hispanics, and Native Americans. A random sampling (163) of DRB1*13-positive individuals from each self-described ethnic group was selected out of a pool of 82,979 unrelated individuals, providing at least an 80% probability of detecting a rare allele that occurred at 1%. These 815 samples were subjected to allele-level SSOP typing and/or DNA sequencing which identified 11 different DRB1*13 alleles. DRB1*1301 and DRB1*1302 were the most common alleles seen in the five major ethnic groups while DRB1*1304 was not detected among Caucasians and DRB1*1305 was not detected among African Americans. DRB1*13 allele diversity was surprisingly more limited among African Americans compared to both Caucasians and Asian/Pacific Islanders. To determine the extent of DRB1*13-DRB3 associations, 504 of these samples expressing only one DRB3-associated DRB1 allele were subjected to PCR-SSOP typing and 14 DRB1*13-DRB3 haplotypes were detected. The distribution revealed that African Americans were significantly different from Caucasians, Asian/Pacific Islanders, and Hispanics. Allele frequency studies such as this further support previous findings that the distribution of HLA types can differ significantly among different ethnic populations.

HLA-DRB1*08, DRB1*03/DRB3*0101, and DRB3*0202 are susceptibility genes for Graves' disease in North American Caucasians, whereas DRB1*07 is protective

Graves' disease is known to be HLA-D associated; however, the primary loci involved remain unclear. We examined HLA genotypes of DRB1 and DQB1 plus DRB3 subtypes using PCR-based sequence-specific priming in two groups of North American (Gainesville, FL; and Toronto, Canada) Caucasian patients with Graves' disease. We stratified patients into those with either early age at onset (<20 yr; 13.1 +/- 4.8 yr; n = 30) and later age at onset of disease (38.8 +/- 9.7 yr; n = 62) and compared the results to 192 normal controls. As expected, we found that DRB1*03 was associated with Graves' disease, but at a higher odds ratios for early-onset than later-onset patients (3.7 vs. 2.2). The frequency of DRB1*08 was also increased in both groups of patients, but significantly so only in patients with early-onset Graves' (P = 0.001; chi2 = 10.8). DRB3 was highly associated with Graves' in both groups of patients (P = 0.009; chi2 = 6.83 and P = 0.0015; chi2 = 10.1, respectively); however, the subtypes of DRB3 revealed differential susceptibilities. Whereas the frequencies of both DRB3*0101 and DRB3*0202 were increased over the entire cohort, that of DRB3*0301 was not. Significant P values were found for DRB3*0101 in patients with early-onset and for DRB3*0202 in patients with later onset of Graves' disease. When the haplotypes of DRB1*03-DRB3 of all subtypes were removed for analysis (all DRB1*03 positive also had DRB3*0101), the frequency of DRB3*0202 remained significantly higher in the patients with later onset of Graves' disease than in controls (P = 0.0043; chi2 = 8.13), but DRB3 was no longer positively associated with the early-onset group. In addition, we found that DRB1*07 was negatively associated with both groups of patients (P = 0.024; chi2 = 5.10 and P = 0.0085; chi2 = 6.93). These data suggest that DRB3*0202 is more likely to be the primary susceptible locus than DRB1*03 for patients with later onset of Graves' disease.

CD4 TCRBV CDR3 analysis in prevalent SLE cases from two ethnic groups

We examined CD4+ T cell TCRBV-CDR3 transcripts from 19 lupus patients and 16 controls to test the hypothesis that CD4+ TCRBV-CDR3 expression in SLE differs from normals. Within the disease group we also performed exploratory analyses to determine the association between risk of oligoclonality and HLA-DRB specificities and the duration of the CDR3 patterns. Oligoclonal patterns consistent with CDR3 restriction were three times more likely in SLE than in controls (OR = 3.7). TCRBV1, BV4, BV5.1, BV7, BV9, BV18 and BV22 gene segment CDR3 patterns of oligoclonality were seen exclusively among lupus patients. HLA-DRB3 increased the risk of oligoclonal expression in SLE. In four patients studied over time, the pattern of TCRBV-CDR3 expression was stable in a second sample obtained 6-14 months later. The increased frequency of CD4+ T cell TCRBV-CDR3 oligoclonal expression in SLE when compared to controls and the persistence of these patterns are consistent with an expanded pool of autoreactive CD4 T cells in SLE which recognize peptides derived from autoantigens. The association of HLA-DRB3 genes with increased risk of CDR3 oligoclonality among the SLE subjects is compatible with the hypothesis that molecules encoded by HLA-DRB3 may facilitate autoantigen recognition by CD4 T cells.