DRB1*03 diversity and DRB3 associations in five major population groups in the United States

The prevalence of HPA-1a alloimmunization and the potential risk of FNAIT depend on both the DRB3*01:01 allele and associated DR-DQ haplotypes

Alloimmunization against human platelet antigen (HPA)-1a during pregnancy can cause foetal/neonatal alloimmune thrombocytopenia (FNAIT) and severe bleeding in the foetus or newborn and likely depends on several factors. HPA-1a alloimmunization is associated with DRB3*01:01, which is associated with several DR-DQ haplotypes. However, it is not known to what extent these haplotypes contribute to the prevalence of HPA-1a alloimmunization. HPA-1a-alloimmunized women, identified in a prospective study, and random donors were typed for selected DRB3, DRB4, DRB1, DQA1 and DQB1 alleles to determine allele and DR-DQ haplotype frequencies. DRB3*01:01 was carried by 94% HPA-1a-immunized women compared to 27% in the general population. In the first population, the DR3-DQ2 haplotype was overrepresented (P < .003). The prevalence of HPA-1a alloimmunization was estimated to be about twice as frequent with DR3-DQ2 compared to DR13-DQ6, together accounting for about 90% of DRB3*01:01-positive individuals. Further, we examined DQB1*02 and DRB4*01:01 alleles for their reported association with HPA-1a alloimmunization, in the context of DR-DQ haplotypes. Since ~ 80% of DQB1*02 alleles are linked to the DR3-DQ2 haplotype, the association might be coincidental. However, the DQB1*02:02-associated DR7-DQ2 haplotype was also overrepresented in alloimmunized women, suggesting a role for this allele or haplotype in HPA-1a alloimmunization. As DRB4*01:01 is predominantly associated with the DR7-DQ2 haplotype in HPA-1a-alloimmunized individuals, the reported association with FNAIT may be coincidental. Typing for DR-DQ haplotypes revealed important genetic associations with HPA-1a alloimmunization not evident from typing individual alleles, and the presence of different DRB3-associated DR-DQ haplotypes showed different prevalence of HPA-1a alloimmunization.

Discovery of HLA-DRB1*03:20 allele in a Taiwanese volunteer hematopoietic stem cell donor and the probable HLA-A, -B, -C and -DRB1 haplotype in association with DRB1*03:20

The allele HLA-DRB1*03:20, a variant of DRB1*03, was first reported to the IMGT HLA database in April 2001 without indication on the ethnicity of the blood donor (Cell ID: HC 125775). We found a Taiwanese volunteer hematopoietic stem cell donor carries DRB1*03:20 by a sequence-based typing (SBT) method. The DNA sequence of DRB1*03:20 is identical to the sequence of DRB1*03:01:01 in exon 2, except a nucleotide substitution at position 341(T→C) (GTT→GCT at codon 85). The nucleotide replacement produced an amino acid variation at residue 85 (V→A). We hypothesize that DRB1*03:20 was probably derived from DRB1*03:01:01 via a nucleotide point mutation event. The probable HLA haplotype in association with DRB1*03:20 was deduced as A*11:02-B*58:01-C*07:02-DRB1*03:20. We here report the Taiwanese/Chinese ethnicity of DRB1*03:20.

Discovery of the novel HLA-DRB1*03:77 allele in a Taiwanese unrelated hematopoietic stem cell donor by a sequence-based typing method and identification of the probable HLA haplotype in association with DRB1*03:77

Here, we report a novel human leucocyte antigen (HLA)-DRB1 allele, DRB1*03:77, discovered in a Taiwanese unrelated volunteer hematopoietic stem cell donor by a sequence-based typing (SBT) method. The DNA sequence of DRB1*03:77 is identical to the DNA sequence of DRB1*03:01:01 in exon 2 except one nucleotide at position 223 (G→C). The nucleotide substitution caused an amino acid replacement at residue 46 (E→Q). The formation of DRB1*03:77 was thought as the result of a nucleotide point mutation. The probable HLA-A, HLA-B and HLA-DRB1 haplotype in association with DRB1*03:77 may be deduced as A*33-B*58-DRB1*03:77. The donor was a Minna Taiwanese whose ancestors came from mainland China.

The cellular immunobiology associated with fetal and neonatal alloimmune thrombocytopenia

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is caused by maternal antibodies that cross the placenta in connection with pregnancy and destroy fetal platelets. Recently, maternal T cell responses associated with FNAIT have been studied at the clonal level. These T cell clones recognize an integrin β3 epitope, which is anchored to the HLA-DRB3∗0101-encoded MHC molecule DR52a. The same MHC allele is strongly associated with FNAIT. As the production of pathological antibodies reactive with fetal platelets is likely dependent on these T cell responses, there exists a potential for preventing FNAIT by targeting these T cells.

Reassessing the role of HLA-DRB3 T-cell responses: evidence for significant expression and complementary antigen presentation

In humans, several HLA-DRB loci (DRB1/3/4/5) encode diverse beta-chains that pair with alpha-chains to form DR molecules on the surface of APC. While DRB1 and DRB5 have been extensively studied, the role of DRB3/4 products of DR52/DR53 haplotypes has been largely neglected. To clarify the relative expression of DRB3, we quantified DRB3 mRNA levels in comparison with DRB1 mRNA from the same haplotype in both B cells and monocytes, observing quantitatively significant DRB3 synthesis. In CD19+ cells, DRB1*03/11/13 was 3.5-fold more abundant than DRB3, but in CD14+ this difference was only two-fold. Monocytes also had lower overall levels of DR mRNA compared with B cells, which was confirmed by cell surface staining of DRB1 and DRB3. To evaluate the functional role of DRB3, tetramer-guided epitope mapping was used to detect T cells against tetanus toxin and several influenza antigens presented by DRB3*0101/0202 or DRB1*03/11/13. None of the epitopes discovered were shared among any of the DR molecules. Quantitative assessment of DRB3-tetanus toxin specific T cells revealed that they are present at similar frequencies as those observed for DRB1. These results suggest that DRB3 plays a significant role in antigen presentation with different epitopic preferences to DRB1. Therefore, DRB3, like DRB5, serves to extend and complement the peptide repertoire of DRB1 in antigen presentation.

Peptides presented in vivo by HLA-DR in thyroid autoimmunity

The association of the major histocompatibility complex (MHC) genes with autoimmune diseases together with the ectopic expression of class II molecules by epithelial cells of the target tissue gives to these molecules a central role in the pathogenesis of the disease, in its regulation and in the persistence of the immune response in situ. HLA-DR molecules expressed by thyroid follicular cells in thyroid autoimmune diseases are compact molecules stably associated with peptides. The nature of these peptides is of vital importance in the understanding of the disease, since these MHC-II-peptide complexes are going to be recognized by both effector and regulatory T cells in situ. In this chapter, we review the current state of the analysis of naturally processed peptides presented by MHC class II molecules in the context of autoimmunity and we discuss our data of natural HLA-DR ligands eluted from Graves' disease affected thyroid glands, from where autoantigen-derived peptides have been identified.

Discovery of HLA-DRB1*0331 in a Taiwanese marrow donor and the importance of sequence-based typing in a rare or previously unrecognized allele

We describe here a novel HLA-DRB1* allele, DRB1*0331, observed from a Taiwanese bone marrow donor using DNA sequence-based typing (SBT) method. The 'new' allele differs from DRB1*0306 and DRB1*0325 by one nucleotide at positions 196 and 227, respectively. Nucleotide mutations caused amino acid substitutions from N to Y at codon 37 and from F to Y at codon 47, as compared with amino acid sequence encoded by the DRB1*030101 allele. The donor was first typed as DRB1*0403/0406/0439/0441/0446/0451/0452 (NMDP code DRB1*04XX) and DRB1*0304/0323/0325 (NMDP code DRB1*03APDA) by sequence-specific oligonucleotide (SSO) typing kit. Subsequent typing of the donor by high-resolution sequence-specific primer (SSP) protocol indicated DRB1*0403 and DRB1*0306. The anomalous result of DRB1*03 was resolved by SBT and recognized as DRB1*0331. We concluded that SSP or SSO alone may mistype a precedent unrecognized allele and that two different typing techniques or SBT may have to be employed to safe guard true HLA typing when rare alleles are encountered at the first time.

Prediction of crossmatch outcome of highly sensitized patients by single and/or multiple antigen bead luminex assay

BACKGROUND

We used a solid-phase assay to identify human leukocyte antigen (HLA) Class I and II specificities in highly reactive sera, and applied this information to predict crossmatch outcome with greater than 90% accuracy.

METHODS

Sera from 20 highly sensitized end-stage renal disease patients reactive to 70-100% of HLA Class I and II antigen panel were analyzed by single and/or multiple antigen flow microparticle bead assay using Luminex platform (Luminex assay). These sera contained antibodies directed against high frequency public HLA class I and/or II epitopes accounting for 70-100% of serum's total reactivity. More than 2,000 complement dependent cytotoxicity (CDC) and 200 flow crossmatches (FLXM) were performed using sera from these patients and deceased donor T and B lymphocytes.

RESULTS

Luminex serum analysis was able to correctly predict outcomes of 95% of T and B cell FLXM. In contrast, predictive values for the CDC T and B cell crossmatches by Luminex serum analysis were only 77% and 75%, respectively. The use of serum analysis in donor selection would have reduced the total number of required FLXM by more than 50%. The frequency of negative T cell FLXM was 56% when donors were selected randomly; however, if serum antibody analysis had been used to preselect the donors by excluding donors that were likely to be positive, the frequency of corresponding negative crossmatches would have increased up to 93%.

CONCLUSION

This approach to donor selection may allow wider geographic sharing of cadaver donor organs without actually performing the crossmatch.

HLA polymorphisms in African Americans with idiopathic inflammatory myopathy: allelic profiles distinguish patients with different clinical phenotypes and myositis autoantibodies

OBJECTIVE

To investigate possible associations of HLA polymorphisms with idiopathic inflammatory myopathy (IIM) in African Americans, and to compare this with HLA associations in European American IIM patients with IIM.

METHODS

Molecular genetic analyses of HLA-A, B, Cw, DRB1, and DQA1 polymorphisms were performed in a large population of African American patients with IIM (n = 262) in whom the major clinical and autoantibody subgroups were represented. These data were compared with similar information previously obtained from European American patients with IIM (n = 571).

RESULTS

In contrast to European American patients with IIM, African American patients with IIM, in particular those with polymyositis, had no strong disease associations with HLA alleles of the 8.1 ancestral haplotype; however, African Americans with dermatomyositis or with anti-Jo-1 autoantibodies shared the risk factor HLA-DRB1*0301 with European Americans. We detected novel HLA risk factors in African American patients with myositis overlap (DRB1*08) and in African American patients producing anti-signal recognition particle (DQA1*0102) and anti-Mi-2 autoantibodies (DRB1*0302). DRB1*0302 and the European American-, anti-Mi-2-associated risk factor DRB1*0701 were found to share a 4-amino-acid sequence motif, which was predicted by comparative homology analyses to have identical 3-dimensional orientations within the peptide-binding groove.

CONCLUSION

These data demonstrate that North American IIM patients from different ethnic groups have both shared and distinct immunogenetic susceptibility factors, depending on the clinical phenotype. These findings, obtained from the largest cohort of North American minority patients with IIM studied to date, add additional support to the hypothesis that the myositis syndromes comprise multiple, distinct disease entities, perhaps arising from divergent pathogenic mechanisms and/or different gene-environment interactions.

High-resolution typing of HLA-DRB1 locus in the Macedonian population

The Macedonian population is of special interest for HLA anthropological study in the light of unanswered questions regarding its origin and relationship with other populations, especially the neighbouring Balkanians. Two studies have been performed to examine HLA molecular polymorphism in the Macedonian population, so far. The present study is the first to be performed in Macedonia using high-resolution sequence-based method for direct HLA typing. The study included 158 unrelated healthy volunteers of Macedonian origin and nationality, having a Christian Orthodox religion. After the simultaneous amplification of exon-2 on both HLA-DRB1 alleles, DNA sequencing was used for genotype assignment. In the 158 samples analysed, all 316 alleles were typed and a total of 29 different DRB1 alleles were detected, with DRB1*1601 being the most frequent allele (14.9%), followed by DRB1*1104 (13.9%). A phylogenetic tree constructed on the basis of the high-resolution data deriving from other populations revealed the clustering of Macedonians together with other Balkan populations (Greeks, Croats, Turks and Romanians) and Sardinians, close to another "European" cluster consisting of the Italian, French, Danish, Polish and Spanish populations. The included African populations grouped on the opposite side of the tree.

HLA class II profile and distribution of HLA-DRB1 and HLA-DQB1 alleles and haplotypes among Lebanese and Bahraini Arabs

The gene frequencies of HLA class II alleles were studied in 95 healthy Lebanese Arab and 72 healthy Bahraini Arab subjects. Our aim was to establish the genetic relationship between Bahraini and Lebanese Arabs in terms of HLA class II gene and haplotype frequencies and to compare these results with frequencies for other countries with populations of Caucasian and non-Caucasian descent. Subjects were unrelated and of both sexes, and HLA-DRB1 and -DQB1 genotyping was done by the PCR sequence-specific primer technique. Comparative analysis of the HLA-DR and -DQ alleles revealed differences in the allelic distribution among Bahraini and Lebanese subjects. Analysis of the 25 HLA-DRB1 alleles that have been investigated showed that the DRB1*040101 and DRB1*110101 alleles were more frequent among Lebanese, whereas DRB1*030101 and DRB1*160101 alleles were more frequent among Bahrainis. Similarly, of the seven HLA-DQB1 alleles analyzed, the presence of DQB1*0201 was more frequent among Bahrainis, whereas DQB1*030101 was more frequent among Lebanese. The DRB1*160101-DQB1*050101 (0.1318 versus 0.0379%) and DRB1*030101-DQB1*0201 (0.1202 versus 0.0321%) haplotypes were more frequent among Bahrainis, while the DRB1*110101-DQB1*030101 (0.3142 versus 0.1198%) and DRB1*040101-DQB1*0302 (0.1416 versus 0.0278%) haplotypes were more frequent in Lebanese subjects. Furthermore, a high prevalence of the DRB1*040101-DRB1*110101-DQB1*0302-DQB1*030101 (12.63 versus 1.35%, P = 0.015) and the homozygous DRB1*110101-DRB1*110101-DQB1*030101-DQB1*030101 (7.37 versus 0.00%, P = 0.046) genotypes was seen among Lebanese, and DRB1*070101-DRB1*160101-DQB1*0201-DQB1*050101 (6.76 versus 0.00%, P = 0.034) was seen more frequently among Bahraini subjects. Our results underline significant differences between these two populations in HLA class II distribution, provide basic information for further studies of major histocompatibility complex heterogeneity among Arabic-speaking countries, and serve as a reference for further anthropological studies.

Distinct but overlapping T helper epitopes in the 37–58 region of SSX-2

Because of their specific expression in tumors of different histological types, the products of the SSX genes are important candidate targets for development of cancer vaccines. We have previously identified two immunodominant SSX-2-derived T cell epitopes recognized by HLA-A2-restricted CD8+ T cells (SSX-2 41-49) and HLA-DR11-restricted CD4+ T cells (SSX-2 45-59), respectively. In this study, we report the identification of an HLA-DR3-restricted epitope mapping to the 37-51 region of SSX-2, overlapping both previously identified epitopes. As about one fifth of individuals from several major ethnic groups express HLA-DR3, the identification of this epitope significantly increases the percent of patients that are expected to mount specific CD4+ T cell responses following vaccination with peptides in this region of SSX-2. Retrieval of multiple overlapping epitopes in a defined region of SSX-2 protein suggests the presence of a "hot spot" for T cell recognition that may prove sufficient for the induction of immune responses.

Polymorphism scan for differences between transmitted and nontransmitted DRB1*030101 alleles outside of exon 2 for type 1 diabetes: The frequency of polymorphisms is similar

DRB1*030101 is a major genetic risk factor for type 1 diabetes mellitus (T1DM) and is the only DRB1*03 allele usually seen in T1DM probands. Approximately 16% of parental DRB1*030101 alleles were not transmitted to T1DM probands in our Genetics of Kidneys and Diabetes study trio families. We performed a polymorphism screen to determine whether variations exist in DRB1*030101 alleles outside of exon 2 that may modify risk for developing T1DM. A combination of long-range and sequence-specific priming polymerase chain reaction was used to amplify a hemizygous template from both transmitted and nontransmitted parental DRB1*030101 chromosomes. Exon 2 DRB1*030101-specific and flanking DRB1-specific primers amplified the entire genomic locus as a 10.6-kb 5' fragment and a 5.3-kb 3' fragment, respectively. All exons and intron/exon borders of introns 1 and 2, all of introns 3-5, and flanking regulatory regions of 32 transmitted and 31 nontransmitted alleles (99% power to detect a 5% minimal allele frequency) were analyzed through fluorescent DNA sequencing. The only polymorphic sites detected, a previously described intron 2 complex dinucleotide repeat and an additional complex repeat approximately 1.8 kb downstream of exon 6, do not significantly differ between T1DM patients and controls in this small data set.

HLA-DRB1 and -DRB3 allele frequencies and haplotypic associations in Koreans

We have investigated the frequencies of human leukocyte antigen-DRB1 (HLA-DRB1) and -DRB3 alleles and DRB1-DRB3 haplotypic associations in 800 Koreans. DRB1 genotyping was done using polymerase chain reaction-sequence-specific oligonucleotide (PCR-SSO) and PCR-single strand conformation polymorphism (SSCP) methods. DRB3 genotyping was done on 447 samples carrying DRB3-associated DRB1 alleles (DRB1*03, *11, *12, *13, and *14) using PCR-SSCP method. The allele frequencies of DRB3*0101, DRB3*0202, and DRB3*0301 were 0.073, 0.136, and 0.120, respectively, and we found one case of a probable new allele (DRB3*01new, 0.001). DRB1-DRB3 haplotypes with frequency (HF) > 0.005 exhibited strong associations between DRB3*0101 and DRB1*1201, *1301, and *1403; between DRB3*0301 and DRB1*1202 and *1302; between DRB3*0202 and DRB1*0301, *1101, *1401, *1405, and *1406 alleles. Most of the DRB1 alleles with frequency > 0.005 were exclusively associated with particular DRB3 alleles with relative linkage disequilibrium values of 1.0, except for DRB1*1201, *1202 and *1301; the rare presence (HF < 0.005) of DRB3*0202 associations were observed for these DRB1 alleles. We also investigated and presented rare DRB1-DRB3 associations in additional 6000 Koreans. Comparison with other ethnic groups revealed that DRB1*0301 and *1301 related DRB1-DRB3 haplotypes vary among different populations, in that Koreans and other Asian populations show less diversity compared with Caucasoids or African Americans.

HLA-DRB1*1101: a significant risk factor for sarcoidosis in blacks and whites

Sarcoidosis is a granulomatous disorder of unknown etiology, associated with an accumulation of CD4+ T cells and a TH1 immune response. Since previous studies of HLA associations with sarcoidosis were limited by serologic or low-resolution molecular identification, we performed high-resolution typing for the HLA-DPB1, HLA-DQB1, HLA-DRB1, and HLA-DRB3 loci and the presence of the DRB4 or DRB5 locus, to define HLA class II associations with sarcoidosis. A Case Control Etiologic Study of Sarcoidosis (ACCESS) enrolled biopsy-confirmed cases (736 total) from 10 centers in the United States. Seven hundred six (706) controls were case matched for age, race, sex, and geographic area. We studied the first 474 ACCESS patients and case-matched controls. The HLA-DRB1 alleles were differentially distributed between cases and controls (P<.0001). The HLA-DRB1*1101 allele was associated (P<.01) with sarcoidosis in blacks and whites and had a population attributable risk of 16% in blacks and 9% in whites. HLA-DRB1-F(47) was the amino acid residue most associated with sarcoidosis and independently associated with sarcoidosis in whites. The HLA-DPB1 locus also contributed to susceptibility for sarcoidosis and, in contrast to chronic beryllium disease, a non-E(69)-containing allele, HLA-DPB1*0101, conveyed most of the risk. Although significant differences were observed in the distribution of HLA class II alleles between blacks and whites, only HLA-DRB1*1501 was differentially associated with sarcoidosis (P<.003). In addition to being susceptibility markers, HLA class II alleles may be markers for different phenotypes of sarcoidosis (DRB1*0401 for eye in blacks and whites, DRB3 for bone marrow in blacks, and DPB1*0101 for hypercalcemia in whites). These studies confirm a genetic predisposition for sarcoidosis and present evidence for the allelic variation at the HLA-DRB1 locus as a major contributor.

Diversity within the DRB1*08 allele family in four populations from a United States hematopoietic stem cell donor database and characterization of five novel DRB1*08 alleles

The frequencies of DRB1*08 alleles within four major United States populations found within a hematopoietic stem cell volunteer donor database were determined by DNA sequencing of over 60 DRB1*08 positive individuals from each group. Seven of 30 known DRB1*08 alleles were identified within this study population (080101, 080201, 080302, 080401, 0806, 0807, and 0811). Each ethnic group was characterized by a different highly prevalent allele: DRB1*080101 in Caucasians; DRB1*080401 in African-Americans; DRB1*080302 in Asians; and DRB1*080201 in Hispanics. The alleles DRB1*080101, DRB1*080201, and DRB1*080401 were present in all four populations. This report also describes five novel DRB1*08 alleles uncovered during routine human leukocyte antigen typing.

DRB1*14 diversity and DRB3 associations in four major population groups in the United States

At least 59 DRB1*14 positive individuals from each of four U.S. population groups, Caucasoids, African Americans, Asians/Pacific Islanders, and Hispanics, were randomly selected from a database of 82,979 individuals. DRB1*14 alleles were identified by DNA sequence analysis using intron-specific primers to obtain complete exon 2 sequences. Only 23% of the known DRB1*14 alleles were detected. DRB1*14011 was the predominant DRB1*14 allele in three populations while Hispanics carried DRB1*1402 and DRB1*1406 more frequently. Asians/Pacific Islanders were the most diversified carrying seven alleles. DRB3*0101, DRB3*02021 and DRB3*0210 were detected in a subset of individuals typed for this locus and 15 DRB1-DRB3 haplotypes were defined. This study completes the exon 2 sequences of previously identified alleles, DRB1*1405-*1408, including the identification of two silent codon 90 variants of DRB1*1407. In addition, two new DRB1*14 alleles, DRB1*1441 and DRB1*1442, are described.