Nomenclature for factors of the HLA system, 2000

Shared molecular amino acid signature in the HLA-DR peptide binding pocket predisposes to both autoimmune diabetes and thyroiditis

There is strong genetic association between type 1A diabetes (T1D) and autoimmune thyroid disease (AITD). T1D and AITD frequently occur together in the same individual, a condition classified as a variant of the autoimmune polyglandular syndrome type 3 (APS3). Because T1D and AITD are individually strongly associated with different HLA class II sequences, we asked which HLA class II pocket sequence and structure confer joint susceptibility to both T1D and AITD in the same individual (APS3v). We sequenced the HLA-DR gene in 105 APS3v patients and 153 controls, and identified a pocket amino acid signature, DRβ-Tyr-26, DRβ-Leu-67, DRβ-Lys-71, and DRβ-Arg-74, that was strongly associated with APS3v (P = 5.4 × 10(-14), odds ratio = 8.38). Logistic regression analysis demonstrated that DRβ-Leu-67 (P = 9.4 × 10(-13)) and DRβ-Arg-74 (P = 1.21 × 10(-13)) gave strong independent effects on disease susceptibility. Structural modeling studies demonstrated that pocket 4 was critical for the development of T1D+AITD; all disease-associated amino acids were linked to areas of the pocket that interact directly with the peptide and, therefore, influence peptide binding. The disease-susceptible HLA-DR pocket was more positively charged (Lys-71, Arg-74) compared with the protective pocket (Ala-71, Gln-74). We conclude that a specific pocket amino acid signature confers joint susceptibility to T1D+AITD in the same individual by causing significant structural changes in the MHC II peptide binding pocket and influencing peptide binding and presentation. Moreover, Arg-74 is a major amino acid position for the development of several autoimmune diseases. These findings suggest that blocking the critical Arg-74 pocket might offer a method for treating certain autoimmune conditions.

Intracellular retention of the NKG2D ligand MHC class I chain-related gene A in human melanomas confers immune privilege and prevents NK cell-mediated cytotoxicity

Most tumors grow in immunocompetent hosts despite expressing NKG2D ligands (NKG2DLs) such as the MHC class I chain-related genes A and B (MICA/B). However, their participation in tumor cell evasion is still not completely understood. Here we demonstrate that several human melanomas (cell lines and freshly isolated metastases) do not express MICA on the cell surface but have intracellular deposits of this NKG2DL. Susceptibility to NK cell-mediated cytotoxicity correlated with the ratio of NKG2DLs to HLA class I molecules but not with the amounts of MICA on the cell surface of tumor cells. Transfection-mediated overexpression of MICA restored cell surface expression and resulted in an increased in vitro cytotoxicity and IFN-gamma secretion by human NK cells. In xenografted nude mice, these melanomas exhibited a delayed growth and extensive in vivo apoptosis. Retardation of tumor growth was due to NK cell-mediated antitumor activity against MICA-transfected tumors, given that this effect was not observed in NK cell-depleted mice. Also, mouse NK cells killed MICA-overexpressing melanomas in vitro. A mechanistic analysis revealed the retention of MICA in the endoplasmic reticulum, an effect that was associated with accumulation of endoH-sensitive (immature) forms of MICA, retrograde transport to the cytoplasm, and degradation by the proteasome. Our study identifies a novel strategy developed by melanoma cells to evade NK cell-mediated immune surveillance based on the intracellular sequestration of immature forms of MICA in the endoplasmic reticulum. Furthermore, this tumor immune escape strategy can be overcome by gene therapy approaches aimed at overexpressing MICA on tumor cells.

Possible interaction between HLA-DRbeta1 and thyroglobulin variants in Graves' disease

Graves' disease (GD) is influenced by two major susceptibility loci, HLA-DR3 and thyroglobulin (Tg). Recently we have shown that specific HLA-DR and Tg gene sequences predispose to Graves' disease. Individuals carrying at least one arginine at position 74 of the DRbeta1 chain (denoted the R- genotype) have a significantly increased risk of GD, as do individuals homozygous for the single nucleotide protein (SNP) in exon 33 of the Tg gene (denoted the CC genotype). Therefore, for the current study we hypothesized that these two genes may interact to influence the etiology of GD. To test this hypothesis, we analyzed the genotypes of 185 Caucasian patients with GD and 143 Caucasian controls for both genes. We tested for an interaction effect, that is, is one gene's effect on GD greater when the other gene is also present than when the other gene is absent? A logistic regression analysis yielded an estimate of 4.31 for the interaction term (p = 0.053). Our results may suggest an interaction between the R- and CC variants in conferring susceptibility to GD. These results, if confirmed, may imply that these two variants interact biologically to increase the odds of GD.

HLA Alleles and Risk of Cervical Intraepithelial Neoplasia Among Southwestern American Indian Women

An increase in cervical intraepithelial neoplasia (CIN) has been described in American Indian women in New Mexico. Differences in human leukocyte antigen (HLA) alleles have been reported in cervical intraepithelial neoplasia (CIN) compared with controls in other populations. We investigated HLA alleles and CIN in Southwest American Indian women. The case control study included 89 women with biopsy-proven CIN II/III (diagnosed November 1994 through October 1997) and 271 similar women with normal cervical epithelium from the same clinics. DRB1, DQB1, and DPB1 alleles were determined using DNA typing techniques. DQA1 and HLA-A allele typing was included for some subjects (randomly chosen n = 37 and n = 163 cases and controls, respectively). We found a decreased risk of CIN with DRB1*1402 (OR 0.5, 95% CI 0.3-0.9) and an increased risk with DRB1*1501 (OR 2.7, 95% CI 0.9-7.3). Additionally, DQA1*0102 was associated with increased risk (OR 4.5, 95% CI 1.3-5.3) and HLA-A*02 with decreased risk (OR 0.4, CI 0.2-0.9). Our findings are discussed along with studies in other populations.

Genetic analysis of families with autoimmune diabetes and thyroiditis: evidence for common and unique genes

CONTEXT

Epidemiological data suggest a common genetic susceptibility to type 1 diabetes (T1D) and autoimmune thyroid disease (AITD).

OBJECTIVE

Our objective was to identify the joint susceptibility genes for T1D and AITD.

DESIGN

We conducted a family-based linkage and association study.

SETTING

The study took place at an academic medical center.

PARTICIPANTS

Participants included 55 multiplex families (290 individuals) in which T1D and AITD clustered (T1D-AITD families).

MAIN OUTCOME MEASURES

We conducted tests for linkage and family-based associations (transmission disequilibrium test) with four candidate genes: human leukocyte antigen (HLA), cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), insulin variable number of tandem repeats (VNTR), and thyroglobulin.

RESULTS

Linkage evidence to HLA appeared when subjects with either T1D or AITD were considered affected [maximum LOD score (MLS), 2.2]. The major HLA haplotype contributing to the shared susceptibility was DR3-DQB1*0201, with DR3 conferring most of the shared risk. The CTLA-4 gene showed evidence for linkage only when individuals with both T1D and AITD were considered affected (MLS, 1.7), and the insulin VNTR showed evidence for linkage when individuals with either T1D or AITD were considered affected (MLS, 1.9); i.e. it may contribute to the familial aggregation of T1D and AITD.

CONCLUSIONS

The HLA class II locus contributes to the shared risk for T1D and AITD, and the major HLA haplotype contributing to this association is DR3-DQB1*0201. Additional non-HLA loci contribute to the joint susceptibility to T1D and AITD, and two potential candidates include the CTLA-4 and insulin VNTR loci.

HLA-B27 polymorphism in Turkish patients with ankylosing spondylitis

The aim of this study was to determine the distribution of human leukocyte antigen (HLA)-B27 subtypes in serologically HLA-B27-positive ankylosing spondylitis (AS) patients and healthy controls from the Turkish population and to compare this with other reports from other populations. We subtyped HLA-B27 in 38 HLA-B27-positive Turkish patients with AS and 47 HLA-B27-positive healthy controls without AS by polymerase chain reaction with specific sequence primers (PCR-SSP). The results demonstrated that: B*2705 was the predominant subtype among both of the patients (71.1%) and controls (68.0%). B*2702 was observed in 26.3% and 32.0% of the patients and controls, respectively. B*2708 subtype was found in 2.6% of the patients but not among the control group. When the distribution of B27 subtypes in Turkish populations was compared with that in other populations, similar frequencies with the Caucasian-Europe groups were noted. However, this should be interpreted carefully because of the small number of individuals in our study.

Analysis of HLA genes in families with autoimmune diabetes and thyroiditis

Type 1 diabetes (T1D) and autoimmune thyroid disease (AITD) are the most common autoimmune endocrine disorders. The similar pathogenesis of T1D and AITD and their tendency to occur together suggest that their etiology may involve common genetic factors. We hypothesized that the human leukocyte antigen (HLA) locus may contribute in part to the joint susceptibility to T1D and AITD. We therefore analyzed a data set of 40 multiplex families in which T1D and AITD clustered ("T1D-AITD families") for linkage and association with the HLA class II locus. We found evidence for linkage of the HLA region to T1D (maximum logarithm of odds score [MLS] = 7.3), to Hashimoto thyroiditis (HT) (MLS = 1.5), and to both (MLS = 3.8). Transmission disequilibrium test analysis revealed significant association of both T1D and AITD with HLA-DR3; however, only T1D was associated with HLA-DR4. We concluded that the finding of evidence for linkage of HLA with HT is in contrast to the strong evidence against linkage found in previous studies of AITD-only families; therefore, it is possible that the AITD phenotype seen in T1D families has a different genetic etiology than the AITD phenotype in AITD-only families; that HLA-DR3 was the major HLA allele contributing to the joint genetic susceptibility to T1D and AITD, whereas other alleles (e.g., DR4) are phenotype specific; and that because the logarithm of odds score for T1D + HT was lower than for T1D alone, additional non-HLA loci must contribute to the shared genetic susceptibility to T1D and AITD.

Arginine at position 74 of the HLA-DR beta1 chain is associated with Graves' disease

Graves' disease (GD) is associated with HLA-DR3 (DRB1*03) in Caucasians, but the exact amino-acid sequence in the DR beta1 chain conferring susceptibility to GD is unknown. Therefore, the aim of our study was to identify the critical sequence among the HLA-DRB1 amino-acid residues occupying the peptide-binding pocket, which conferred susceptibility to GD. We sequenced the HLA-DRB1 locus in 208 Caucasian GD patients and 149 Caucasian controls. Sequence analysis showed an increased frequency of DR beta-Arg-74 in GD patients compared to controls (41.8 and 13.4%, respectively; P=2.3 x 10(-8), OR=4.6). Moreover, subset analyses showed that DR beta-Arg-74 was also significantly more frequent in the HLA-DR3 negative GD patients than in controls (7.6 vs 0.8%, P=0.02, OR=10.5), suggesting that the association with DR beta-Arg-74 is independent of the association with HLA-DR3. Structural modeling studies demonstrated that the change at position 74 from the neutral amino acids Ala or Gln to the positively charged amino-acid Arg significantly modifies the three-dimensional structure of the DR peptide-binding pocket. Our results suggested that structural heterogeneity of the DR beta-chain peptide-binding pocket P4 at residue 74 predispose some at risk individuals to GD.

The contribution of immune regulatory and thyroid specific genes to the etiology of Graves' and Hashimoto's diseases

The autoimmune thyroid diseases (AITD) are complex diseases which are caused by an interaction between susceptibility genes and environmental triggers. Genetic susceptibility in combination with external factors (e.g. dietary iodine) are believed to initiate the autoimmune response to thyroid antigens. Abundant epidemiological data, including family and twin studies, point to a strong genetic influence on the development of AITD. Various techniques have been employed to identify the genes contributing to the etiology of AITD, including candidate gene analysis and whole genome screening. These studies have enabled the identification of several loci (genetic regions) that are linked with AITD, and in some of these loci putative AITD susceptibility genes have been identified. Some of these genes/loci are unique to Graves' disease (GD) and Hashimoto's thyroiditis (HT) and some are common to both diseases, indicating that there is a shared genetic susceptibility to GD and HT. The putative GD and HT susceptibility genes include both immune modifying genes (e.g. HLA, CTLA-4) and thyroid specific genes (e.g. TSHR, Tg). Most likely these loci interact and their interactions may influence disease phenotype and severity.

Differential expression of HLA class II genes associated with disease susceptibility and progression in rheumatoid arthritis

OBJECTIVE

Rheumatoid arthritis (RA)-associated HLA class II genes are assumed to promote susceptibility to and/or progression of the disease. Among the various modes of action proposed so far is the effect of the differential expression of HLA class II genes in different types of antigen-presenting cells on the Th1/Th2 balance. The aim of this study was to investigate the differential expression of genes encoded within the RA-associated HLA-DR4 superhaplotype and within the neutral DR7 and DR9 superhaplotypes.

METHODS

The promoters encoded within these 3 haplotypes were first analyzed for sequence polymorphisms. To test for functional consequences, we assumed that the binding of nuclear factors to the promoter elements was correlated with the transcription activity, and we used surface plasmon resonance technology. To that end, oligonucleotides representing the polymorphic regulatory sequences and nuclear extracts from a monocyte cell line and a B cell line were used.

RESULTS

While the promoters of the highly polymorphic HLA-DRB1*04, *07, and *09 alleles showed comparable binding of nuclear factors, differential binding was observed for the 2 promoters that drive the relatively nonpolymorphic DRB4 alleles in linkage disequilibrium with DRB1. Interestingly, analysis of RA patients positive for DR4, DR7, and DR9 revealed the segregation of radiographic progression with the stronger of the 2 DRB4 promoters, independent of the DRB1 allele. Moreover, DRB1*04 alleles in RA patients showed a reduced association with the DRB4 splice variant, completely preventing DRB4 expression.

CONCLUSION

Our findings represent the first evidence of a correlation between the differential expression of HLA class II genes and both the susceptibility and the progression of RA.

Searching for the autoimmune thyroid disease susceptibility genes: from gene mapping to gene function

The autoimmune thyroid diseases (AITD) are complex diseases that are caused by an interaction between susceptibility genes and environmental triggers. Genetic susceptibility, in combination with external factors (e.g., dietary iodine), is believed to initiate the autoimmune response to thyroid antigens. Abundant epidemiological data, including family and twin studies, point to a strong genetic influence on the development of AITD. Various techniques have been used to identify the genes contributing to the etiology of AITD, including candidate gene analysis and whole genome screening. These studies have enabled the identification of several loci (genetic regions) that are linked with AITD, and in some of these loci putative AITD susceptibility genes have been identified. Some of these genes/loci are unique to Graves' disease (GD) and Hashimoto's thyroiditis (HT), and some are common to both diseases, indicating that there is a shared genetic susceptibility to GD and HT. The putative GD and HT susceptibility genes include both immune modifying genes (e.g., human leukocyte antigen, cytotoxic T lymphocyte antigen-4) and thyroid-specific genes (e.g., TSH receptor, thyroglobulin). Most likely these loci interact, and their interactions may influence disease phenotype and severity. It is hoped that in the near future additional AITD susceptibility genes will be identified and the mechanisms by which they induce AITD will be unraveled.

Familial bipolar disorder and multiple sclerosis: a three-generation HLA family study

The coexistence of bipolar disorder (BD) and multiple sclerosis (MS) is well known. Manic symptoms may represent initial symptoms of MS, at least in some cases, and follow the MS-HLA phenotype frequencies. The purpose of this study was to examine the possible relation of BD and MS based on an HLA family study of a woman with BD and comorbid MS, with family history of BD. Five members of the family from three generations (the patient, her mother, her brother, and her two daughters) were examined regarding the two disorders and the HLA class I and II specificities, performed by serology and molecular techniques. Her deceased father, her brother, and her older daughter suffered from BD. Moreover, in her brother, BD and MS comorbidity was diagnosed. The three affected members and the nonaffected grandmother share the same class I and II, HLA-A2, B18, CW8, DR2, DQ1 haplotype. The shared class II, HLA-DR2, DQ1 haplotype among affected individuals, which is well known to be associated with MS in Caucasians, suggests a possible susceptibility locus for BD, mapped on chromosome 6, very close to the HLA region, underlying the clinical comorbidity of the two disorders.

Use of a neural network to assign serologic specificities to HLA-A, -B and -DRB1 allelic products

A computational method was used to predict the serologic specificities of HLA molecules encoded by the HLA-A, -B, and -DRB1 loci. The polypeptide sequences of a subset of alleles (numbering 149) with well-defined serologic assignments were used to train a neural network to predict broad and split serologic assignments for each HLA allelic product. The resultant neural network assignments were compared with those of a validation set containing the sequences of 74 HLA-A, 175 HLA-B, and 117 HLA-DRB1 alleles that had previous serologic test assignments but were not part of the training set. The network was able to correctly predict at least one of the serologic assignments of the majority of the validation alleles (99% of the HLA-A set, 86% HLA-B, 94% HLA-DRB1). The remainder received either no assignment (1% HLA-A, 13% HLA-B, 5% HLA-DRB1) or a different but closely related assignment (1% HLA-B and -DRB1). Overall, the variation in serologic assignment by the network appeared comparable to the assignments seen among different laboratories using serologic techniques. When used to predict the serologic assignments of 393 HLA alleles without known serologic types, the network was able to predict assignments for most alleles (95% HLA-A, 85% HLA-B, 96% HLA-DRB1). The majority of these assignments were consistent with assignments predicted by sequence homologies with known alleles. The remainder did not receive an assignment and likely represent new combinations of epitopes.

Identification of a new HLA-DRB1 allele, DRB1*0321

This communication reports the identification of a new HLA-DRB1*03 allele identified in three members of a Caucasian French family. This new allele has been officially named HLA-DRB1*0321 by the World Health Organization Nomenclature Committee. The complete exon 2 sequence of DRB1*0321 is identical to that of DRB1*0307 except for the first and second nucleotides of codon 37 (TT replacing AA), which lead to the substitution of a tyrosine for a phenylalanine (AAC-->TTC at position 37). The family study showed that this new allele was transmitted into the HLA-A*0101/09, -B*0801/14, -Cw*0701, -DRB1*0321, -DRB3*0101, -DQB1*0503 and -DPB1*0401 haplotype. The complete exon 2 sequence of this new allele has been previously deposited in the EMBL Sequence Database under accession number AF297266.

HLA diversity: detection and impact on unrelated hematopoietic stem cell donor characterization and selection

Matching of patient and unrelated donor for HLA molecules significantly decreases the probability of graft rejection, graft vs. host disease, and transplant-related mortality in hematopoietic stem cell transplantation. A significant challenge in the identification of matched donors is the diversity of the HLA system. Almost 1500 alleles have been identified at 12 HLA loci. Significant progress has been made in the application of DNA-based testing to identify this diversity in patients and unrelated volunteer donors; however, the resolution of registry testing remains limited by the need to test many donors inexpensively. Thus, the transplant center must predict which donor might be a match for their patient using incomplete typing information. Design of a typing strategy based on knowledge of allele and haplotype frequencies is critical to speed donor identification. A further challenge is to compare patient HLA assignments to the over 7.7 million volunteer donors on registries carrying both DNA and serologic assignments. The links between alleles and serologic specificities remain unclear in many cases and complicate the design of computer algorithms used to match patients and donors. Finally, since few patients will find donors who are allele matched for all HLA loci, studies are underway to understand which of the HLA loci are most critical to match and to define rules of permissive mismatching to achieve an acceptable outcome.

The correlation between ovomucoid-derived peptides, human leucocyte antigen class II molecules and T cell receptor-complementarity determining region 3 compositions in patients with egg-white allergy

BACKGROUND

Food allergies are more prevalent in children, due to the immature gastrointestinal epithelial membrane barrier allowing more proteins through the barrier and into circulation. Ovomucoid (OM) is one of the major allergens that is found in egg white.

OBJECTIVE

The aim of this study was to determine T cell epitopes, antigen-presenting human leucocyte antigen (HLA) class II molecules of the T cell lines (TCLs) and T cell clones (TCCs), and complementarity determining region (CDR) 3 loops of the T cell receptor (TCR) alpha and beta chains of the TCCs specific to OM.

METHODS

We established TCLs and TCCs specific to OM from peripheral blood mononuclear cells (PBMCs) of four atopic patients with egg-white allergy using a mixture of a panel of overlapping synthetic peptides corresponding to the amino acid sequence of the entire OM. We identified the T cell epitopes by antigen-induced proliferative responses, antigen-presenting molecules using allogeneic PBMCs and CDR3 loops of the TCR alpha and beta chains by cloning and sequence analysis.

RESULTS

The TCLs and TCCs responded to seven different peptides, and their antigen-presenting molecules were different from each other. Sequence analysis of the TCR alpha and beta gene usage of the TCCs showed marked heterogeneity, and the usage of the CDR3 loop of the TCCs involved heterogenous amino acid residues. Interestingly, TCCs 'IH3.3' and 'YT6.1' recognized the same OM peptides, and had the same TCR Vbeta-Jbeta gene usage. Considering that peptide motifs bind to HLA class II molecules, the electrically charged residue (positive or negative) on the CDR3alpha and the CDR3beta loops of TCR of TCC may form ionic bonds with a charged residue on the HLA class II molecules-peptide complex.

CONCLUSIONS

TCCs that have the same TCR gene usage were established from patients who had shown similar hypersensitivity-type, indicating that antigen recognition by a specific TCR is closely associated with the characteristics of each patient's symptoms.

Relative HLA-DRB1*04 allele frequencies in five United States populations found in a hematopoietic stem cell volunteer donor registry and seven new DRB1*04 alleles

The frequencies of 29 HLA-DRB1*04 alleles were determined for five major U.S. populations found within a hematopoietic stem cell volunteer donor registry. One hundred sixty-one DRB1*04 positive individuals from each of the self-described groups, Caucasians, African-Americans, Asian/Pacific Islanders, Hispanics, and Native Americans, were randomly chosen from a database of 82,979 unrelated persons. Subjected to polymerase chain reaction-sequence-specific oligonucleotide probe (PCR-SSOP) typing, these 805 individuals carried a total of ten different DRB1*04 alleles, ranging from DRB1*0401 to DRB1*0411 with DRB1*0409 conspicuously absent from all five groups. The distribution of DRB1*04 alleles varied among the groups, with DRB1*0401 being predominant in Caucasians, African-Americans, and Native Americans. DRB1*0404 and DRB1*0407 were the two most commonly observed alleles in Hispanics, whereas DRB1*0405 and DRB1*04031 were most common in Asian/Pacific Islanders. The remaining 18 DRB1*04 alleles known at the time of the study were not observed. Although not observed in the frequency study, seven previously unreported DRB1*04 alleles are also described.

HLA B27 polymorphism in Western India

We have characterized HLA B27 alleles in a sample population of Maharastra, Western Indians (n = 51), with the aim to investigate the different subtypes present among this population. The study was carried out using polymerase chain reaction with sequence-specific primers (PCR-SSP) and reverse line strip (RLS) techniques. Significant new findings have arisen from this study: B*2704, B*2705, B*2707, B*2708 and B*2714 alleles were found to be present, and two novel B27 alleles, B*2708 and B*2714, were found in this Indian population. In addition, B*2714 was observed in a patient with ankylosing spondylitis. This association has not been previously reported in ethnic groups from India.

The influence of human leucocyte antigen (HLA) genes on autoimmune thyroid disease (AITD): results of studies in HLA-DR3 positive AITD families

OBJECTIVE

Population-based, case-control studies have consistently shown association of Graves' disease (GD) with human leucocyte antigen (HLA)-DR3 in Caucasian populations. HLA association studies in Hashimoto's thyroiditis (HT) have also suggested an association with DR3, as well as with other HLA alleles. In contrast, HLA linkage studies in autoimmune thyroid disease (AITD) have been largely negative. The aim of the present study was to investigate the role of HLA in AITD and to explain the observed associations, but lack of linkage, by examining only AITD families with the associated allele, DR3.

PATIENTS

We studied 99 probands (60 with GD and 39 with HT) from 99 multiplex, multigenerational Caucasian AITD families, and 135 age- and sex-matched Caucasian controls in association studies. In addition, a dataset of 34 Caucasian AITD families (out of the 99 families) with HLA-DR3 positive probands were analysed in linkage studies.

DESIGN

HLA typing was performed using the technique of group-specific polymerase chain reaction-amplification with restriction enzyme digestion. Whole genome screening was performed using the ABI microsatellite panels. For fine mapping of the HLA region, we used the following markers: D6S276, D6S464, D6S439, D6S273, tumour necrosis factor alpha and D6S1610. LOD scores were calculated using the LIPED and GeneHunter programs.

RESULTS

Case-control association analyses using the probands from our 99 Caucasian families showed an association of GD with DRB1*03 [P = 0.00032, relative risk (RR) = 3.4]. Linkage analysis for the HLA region in the 34 DR3 positive AITD families showed negative LOD scores throughout the region. The two-point LOD score at marker D6S273 (the closest to HLA-DRB1) was -3.0, and the multipoint LOD score was -7.6, demonstrating strong evidence against linkage to the HLA region in the subset of DR3 positive families. Whole genome screening in the subset of 34 DR3 positive families revealed one locus showing evidence for linkage to AITD: D3S1580 on chromosome 3q27 with a maximum two-point LOD score of 2.1.

CONCLUSIONS

The HLA locus did not cosegregate with disease in DR3 positive families, suggesting that HLA genes are not major genes for AITD expression even within DR3 positive families; Hence, although HLA-DR3 was associated with GD in the probands, it was most likely a modulating gene and not causative; and, as the DR3 positive families showed evidence for linkage with D3S1580, it may imply that the DR3 gene modulated the effect of a susceptibility gene within the D3S1580 locus.

Comparative genomic analysis in the region of a major Plasmodium-refractoriness locus of Anopheles gambiae

We have sequenced six overlapping clones from a library of bacterial artificial chromosome (BAC) clones derived from a laboratory strain of the mosquito, Anopheles gambiae, the major vector of human malaria in Africa. The resulting uninterrupted 528-kb sequence is from the 8C region of the mosquito 2R chromosome, at or very near the major refractoriness locus associated with melanotic encapsulation of parasites. This sequence represents the first extensive view of the mosquito genome structure encompassing 48 genes. Genomic comparison reveals that the majority of the orthologues are found in six microsyntenic clusters in Drosophila melanogaster. A BAC clone that is wholly contained within this region demonstrates the existence of a remarkable degree of local polymorphism in this species, which may prove important for its population structure and vectorial capacity.

Preliminary evidence that an endogenous retroviral long-terminal repeat (LTR13) at the HLA-DQB1 gene locus confers susceptibility to Addison's disease

OBJECTIVE

Addison's disease is associated with particular haplotypes of the human leucocyte antigen (HLA) region [DQA1*0501-DQB1*0201 (DQ2) and DQA1*0301-DQB1*0302 (DQ8)]. This locus harbours several human endogenous retroviral (HERV) long-terminal repeats (LTR). LTRs within the HLA region have been shown to confer additional susceptibility to type 1 diabetes and rheumatoid arthritis.

DESIGN

We investigated the role of LTR3 and LTR13, both of which are located adjacent to the DQB1 gene, in Addison's disease.

PATIENTS

Eighty-seven patients and 160 controls were genotyped for HLA-DQA, -DQB, and the presence or absence of LTR3 and LTR13.

RESULTS

Significantly more patients' HLA alleles than those of controls carried the LTR13 insertion (19.0% vs. 10.6%, P = 0.0143), whereas there was only a trend for LTR3 (allele-wise chi-squared test: P = 0.0941). Both, LTR3 and LTR13 are in strong linkage disequilibrium with DQ8, which itself was significantly more frequent in patients than in controls (29.9% vs. 15.0%, P = 0.0089). However, significantly more alleles of DQ8+ patients than of DQ8+ controls carried the LTR13 insertion (44.2% vs. 18.8%, P = 0.0119), whereas we did not observe any difference for LTR3 in the DQ8+ subset (30.5 vs. 23.1%, P = 0.9416).

CONCLUSIONS

We have found preliminary evidence that the endogenous retroviral element DQ-LTR13, but not LTR3, is associated with Addison's disease. LTR13 appears to enhance HLA-DQ8 mediated disease risk. This retroviral insertion therefore might represent a novel susceptibility factor in Addison's disease, but these findings need to be confirmed in a larger data set.

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.

Molecular analysis of HLA-DRB1, DQA1, DQB1, DQ promoter polymorphism and extended class I/class II haplotypes in the Seri Indians from Northwest Mexico

The study of the genetics of the Major Histocompatibility Complex (MHC) in Amerindians is of great value in understanding the origins and migrations of these native groups, as well as the impact of immunogenetics on the epidemiology of diseases affecting these populations. We analyzed, using Polymerase Chain Reaction and Sequence Specific Oligonucleotide Probes (PCR-SSOP), DRB1, DQA1, DQB1 alleles and the promoter regions of DQA1 and DQB1 genes in 31 unrelated and 24 related Seri, a Mexican Indian group, from the state of Sonora (Northwest Mexico). The class II genotypes of this population were found to be in genetic equilibrium. The allele frequency (AF) of the prevalent DRB1 alleles were DRB1*0407 (48.4%), DRB1*0802 (33.9%) and DRB1*1402 (16.1%). The most frequent DQA1 and DQB1 alleles were DQA1*03011 (AF = 50.00%), DQA1*0401 (AF = 33.87%) and DQA1*0501 (AF = 16.13%); DQB1*0302 (AF = 50.00%), DQB1*0402 (33.87%) and DQB1*0301 (16.13%); which were in combination with DRB1*0407, DRB1*0802 and DRB1*1402, respectively. Three QAP and three QBP alleles were present (QAP 3.1, 4.1, 4.2; QBP 3.1, 3.21, 4.1) associated with the typical published DQA1 and DQB1 alleles. Four class II haplotypes were present in family members: DRB1*0407-QAP-3.1-DQA1*03011-QBP-3.21-DQB1*0302; DRB1*0802-QAP-4.2-DQA1*0401-QBP-4.1-DQB1*0402; DRB1*1402-QAP-4.1-DQA1*0501-QBP-3.1-DQB1*0301 and DRB1*0701-QAP-2.1-DQA1*0201-QBP-2.1-DQB1*0201. The family data were used to confirm extended haplotypes. A total of 21 haplotypes were found when A* and B* loci were also considered. The three most frequent combinations included A*0201-B*3501-DRB1*0407, A*3101-B*5101-DRB1*0802, and A*0201-B*40-DRB1*1402.

HLA-A and HLA-B in Kenya, Africa: allele frequencies and identification of HLA-B*1567 and HLA-B*4426

HLA-A and HLA-B alleles of a population from Kenya, Africa were examined by sequencing exon 2 and exon 3 DNA and typing using a Taxonomy-based Sequence-analysis (TBSA) method. Extensive diversities were observed at both HLA-A and HLA-B loci in this population. Forty-one HLA-A alleles were identified from 159 unrelated individuals. The most frequently observed alleles were A*6802 (11.64%), A*02011/09 (9.75%), A*7401/02 (9.43%), A*3001 (7.86%), A*3002 (7.23%) and A*3601 (6.6%). Forty-nine HLA-B alleles were identified in 161 unrelated individuals, including two novel alleles, B*1567 and B*4426. The most frequently observed HLA-B alleles were B*5301 (9.01%), B*5801 (8.38%), B*4201 (7.76%), B*1503 (7.14%), B*1801 (6.21%), and B*5802 (5.90%). The most frequently observed HLA-A-B haplotypes were A*3601-B*5301 (3.55%) and A*3001-B*4201 (3.19%), followed by A*7401/02-B*5801 (2.84%), A*7401/02-B*5802 (2.84%) and A*02011/09-B*1503 (2.13%). Linkage disequilibrium and chi2 analysis showed the association of these HLA-A-B haplotypes at the antigen level to be significant. The frequencies of HLA-A and HLA-B alleles from the Kenyan population were compared with that of a population from Cameroon. The difference in allele and haplotype frequency distributions partly reflected the different ethnic composition of these two African populations.

Distribution of TAP gene polymorphisms and extended MHC haplotypes in Mexican Mestizos and in Seri Indians from northwest Mexico

The study of the genetic structure is very useful for investigating the biological significance of polymorphism and may provide clues to understand population origins. We present TAP1/TAP2 gene analysis in the Seri indians from Sonora, and in Mestizos from the highlands of Mexico. Thirty-two Seri and 89 Mestizos were studied. TAP genes were typed using the ARMS-PCR technique. The most frequent alleles in Seri were: TAP1*0101/02, (68.8%); TAP1*02011/02012, (31.2%); TAP2*0201, (38.7%) and TAP2*0101, (29.0%). TAP1*0301, TAP1*0401, TAP2*0102 TAP2*0103 and TAP2H were absent in them. For Mestizos, the prevalent alleles were: TAP1*0101/02 (75.8%); TAP1*02011/12 (20.3%); TAP2*0101 (45.4%) and TAP2*0201 (29.3%). These results are similar to those found in Kaingang and Caucasians from Brazil, four Mediterranean, other Caucasians, two Oriental and one African group. In Seri, the extended prevalent haplotypes are typically Amerindian, such as TAP1*0101/2-TAP2*0201-QBP3.21-DQB1*0302-QAP*3.1-DQA1*03011-DRB1*0407-B*3501-A*0201 (HF = 16.6%). Thirty-two extended haplotypes were found in Seri, although TAP contributed scarcely to diversity. Mestizos show Amerindian and Caucasian combinations. No difference was detected in the distribution of amino acids in the individual variable sites, between both groups. These findings are the basis for further anthropological studies and to explore the contribution of TAP genes to disease expression in Mexicans.

Seven new HLA-B alleles associated with antigens in the B7 CREG

This paper describes seven novel HLA-B alleles. Five of these new alleles contain polymorphic motifs previously reported in HLA-B alleles, suggesting an origin resultant from a gene conversion mechanism. B*0723 contains a polymorphism previously unreported in class I HLA molecules. B*4105 contains a nucleotide substitution previously unreported in class I HLA molecules, which encodes a protein sequence previously reported only in HLA-C locus alleles.

Eight new HLA-A alleles associated with antigens in the A2 CREG

This report describes eight novel HLA-A alleles. Seven of these new alleles contain substitutions previously reported in other HLA-A alleles, suggesting an origin resulting from a gene conversion mechanism. Of these seven, A*2431 contains a substitution previously associated with a larger polymorphic motif. A*0247 contains a substitution at a previously polymorphic position, but encodes an amino acid change previously unreported in any HLA-A, -B or -C alleles.

Description of six new HLA-B alleles in the 5C CREG including a B*58 intron two sequence

Five of the six novel HLA-B alleles described in this report contain polymorphic motifs previously reported in HLA-B alleles, suggesting an origin resultant from a gene conversion mechanism. The sixth allele, B*35012, contains a polymorphism previously unreported in HLA-B molecules. In addition to previously reported polymorphisms, B*5806 carries a previously unreported intronic substitution in a sequencing primer annealing site.

FIMM, a database of functional molecular immunology: update 2002

FIMM database (http://sdmc.krdl.org.sg:8080/fimm) contains data relevant to functional molecular immunology, focusing on cellular immunology. It contains fully referenced data on protein antigens, major histocompatibility complex (MHC) molecules, MHC-associated peptides and relevant disease associations. FIMM has a set of search tools for extraction of information and results are presented as lists or as reports.

Combination of HLA-A and HLA class II alleles controls the susceptibility to rheumatoid arthritis

Two hundred and four unrelated Japanese patients with rheumatoid arthritis (RA) were typed for HLA by serological typing and DNA typing. The serological typing revealed that frequencies of HLA-A11, DR4, DR53 and DQ4 were increased and those of DR8 and DQ1 were decreased in the patients. The DNA typing has precisely defined the disease-associated HLA class II alleles; DRBl*0405, DQAl*03 and DQBl*0401 showed positive associations, while negative associations were found with DRBl*0803, DQAl*0103 and DQBl*0601. The risk for RA was found to be closely associated with particular amino acid sequences of DR-beta chain, including glycine residue at the 86th position in addition to those between 70 and 74, which are known to confer binding specificity and affinity to antigenic peptides. The observation that the frequency of HLA-A11 was increased in the DRBl*0405-positive patients suggested the interaction of these two alleles in the susceptibility to RA. On the other hand, the frequency of DPB1*0201 was increased in the DRBl*0405-negative patients and the frequency of HLA-A2 was increased in the DPBl*0201-positive patients, especially in the younger onset group. These findings suggested that the combination of HLA-A2 and DPBl*0201 may confer the susceptibility in the DRBl*0405-negative patients. Our results suggested the possibility that the susceptibility to RA is controlled by the interaction of HLA-A and DRBl genes or by that of HLA-A and DPBl genes in different patient subgroups.

African diversity from the HLA point of view: influence of genetic drift, geography, linguistics, and natural selection

This study investigates the influence of different evolutionary factors on the patterns of human leukocyte antigen (HLA) genetic diversity within sub-Saharan Africa, and between Africa, Europe, and East Asia. This is done by comparing the significance of several statistics computed on equivalent population data sets tested for two HLA class II loci, DRB1 and DPB1, which strongly differ from each other by the shape of their allelic distributions. Similar results are found for the two loci concerning highly significant correlations between geographic and genetic distances at the world scale, high levels of genetic diversity within sub-Saharan Africa and East Asia, and low within Europe, and low genetic differentiations among the three broad continental areas, with no special divergence of Africa. On the other hand, DPB1 behaves as a neutral polymorphism, although a significant excess of heterozygotes is often observed for DRB1. Whereas the pattern observed for DPB1 is explained by geographic differentiations and genetic drift in isolated populations, balancing selection is likely to have prevented genetic differentiations among populations at the DRB1 locus. However, this selective effect did not disrupt the high correlation found between DRB1 and geography at the world scale, nor between DRB1 and linguistic differentiations at the African level.

Genetic variability, molecular evolution, and geographic diversity of HLA-B27

HLA-B27 represents a family of 23 closely related alleles (B*2701-23) that differ at 24 amino acid positions. The pattern of polymorphisms of B27 was studied, with special reference to synonymous (Ks) and nonsynonymous (Ka) divergence among alleles. B27 alleles are characterized by the enhanced rate of nonsynonymous nucleotide substitution in the peptide-binding region (PBR). The percentage of substitutions between each of the B27 pairs ranges from 0.2%-3% in exons 2-3 to 1.8%-20.1% in the PBR. A phylogenetic analysis of all B27 alleles is described in order to identify subtypes with a common evolutionary history. These results, together with the phylogenetic trees obtained from the comparison between exons 2-3 and PBR indicate that polymorphism of B27 is selectively maintained. Most of the differences are clustered in the C/F pocket affecting the specific binding of antigenic peptides. Gene conversion and point mutation are the most important mechanisms responsible for B27 diversification. The interaction of selection, genetic drift, and recombination events is important for generating polymorphism at B27 alleles. We analyzed a large extended B27 positive population from different parts of the world. Our results indicate that B27 subtypes differ in their ethnic distribution, which may be the result of different genetic and geographical origins. Different factors such as genetic drift, bottleneck effect, and admixture among populations could contribute to the genetic constitution of B27. The striking correlation between the structural features of B27 and the ethnic distribution of these subtypes suggests a model of strong directional evolution, in which the subtypes could have arisen from B*2705.

Genetic link between Asians and native Americans: evidence from HLA genes and haplotypes

We have been studying polymorphisms of HLA class I and II genes in East Asians including Buryat in Siberia, Mongolian, Han Chinese, Man Chinese, Korean Chinese, South Korean, and Taiwan indigenous populations in collaboration with many Asian scientists. Regional populations in Japan, Hondo-Japanese, Ryukyuan, and Ainu, were also studied. HLA-A, -B, and -DRB1 gene frequencies were subjected to the correspondence analysis and calculation of DA distances. The correspondence analysis demonstrated several major clusters of human populations in the world. "Mongoloid" populations were highly diversified, in which several clusters such as Northeast Asians, Southeast Asians, Oceanians, and Native Americans were observed. Interestingly, an indigenous population in North Japan, Ainu, was placed relatively close to Native Americans in the correspondence analysis. Distribution of particular HLA-A, -B, -DRB1 alleles and haplotypes was also analyzed in relation to migration and dispersal routes of ancestral populations. A number of alleles and haplotypes showed characteristic patterns of regional distribution. For example, B39-HR5-DQ7 (B*3901-DRB1*1406-DQB1*0301) was shared by Ainu and Native Americans. A24-Cw8-B48 was commonly observed in Taiwan indigenous populations, Maori in New Zealand, Orochon in Northeast China, Inuit, and Tlingit. These findings further support the genetic link between East Asians and Native Americans. We have proposed that various ancestral populations in East Asia, marked by different HLA haplotypes, had migrated and dispersed through multiple routes. Moreover, relatively small genetic distances and the sharing of several HLA haplotypes between Ainu and Native Americans suggest that these populations are descendants of some Upper Paleolithic populations of East Asia.

Increased prevalence of autoimmune thyroid disease in patients with type 1 diabetes

BACKGROUND

Type 1 diabetes mellitus is frequently associated with other autoimmune diseases. The occurrence of common features of autoimmune diseases and the coassociation of multiple autoimmune diseases in the same individual or family supports the notion that there may be common genetic factors.

METHODS

To investigate potential clustering of autoimmune thyroid disease (ATD) among type 1 diabetes patients and the contribution of common susceptibility genes to this, HLA DR/DQ alleles as well as antithyroid autoantibodies were measured in 115 Korean patients with type 1 diabetes and their 96 first-degree family members.

RESULTS

Twenty-five percent of the patients had ATD, whereas 3 of 36 (8%) age-matched normal controls had ATD (RR = 3.7, p < 0.05). Twenty-six of ninty-six (27%) type 1 diabetes family members had ATD. No differences in the distribution of HLA alleles/haplotypes and genotypes between the patients with and without ATD were found.

CONCLUSION

From this finding, we could assess that individuals with type 1 diabetes and their relatives frequently develop ATD, perhaps due to common susceptibility genes that are shared among first degree relatives.