DQ Region Research Articles

DQA-DQB linkage in Old World monkeys.

The MHC DQ region in nonhuman primates, as in humans, consists of alpha and beta chains that are polymorphic with strong linkage disequilibrium between certain DQA-DQB alleles. Not only are contemporary HLA class II allelic variants present in evolutionarily distant species, but we demonstrate that linkages between loci also bear ancient roots. In unrelated baboons (Papio cynocephalus anubis) and family segregation analysis of pigtailed macaques (Macaca nemestrina) we found cis-linkages between DQA1*01 and DQB1*05 or *06, between DQA1*05 and DQB1*03, and between DQA1*03 and DQB1*03 alleles, all of which are also prominent in modern humans. In contrast, one linkage that has not been seen in humans, between DQA1*05 and DQB1*06 alleles, was also found. These patterns of selective linkage disequilibrium imply evolutionary mechanisms following the divergence of species that constrain the diversity of haplotypes which evolve.

Genetic and familial aspects of narcolepsy.

Narcolepsy-cataplexy is a disabling sleep disorder characterized by excessive daytime sleepiness and abnormal REM sleep. The development of human narcolepsy involves environmental factors acting on a specific genetic background. The importance of environmental factors is evidenced by the reported 25 to 31% of monozygotic twins who are concordant for narcolepsy. One of the predisposing genetic factors is located in the MHC DQ region. More than 85% of all narcoleptic patients with definite cataplexy share a specific HLA allele, HLA DQB1*0602 (most often in combination with HLA DR2), compared with 12 to 38% of the general population, as evaluated in various ethnic groups. Genetic factors other than HLA are also likely to be involved. Even if genuine multiplex families are rare, 1 to 2% of the first-degree relatives of narcolepsy patients manifest the disorder, compared with 0.02 to 0.18% in the general population. Studies using a canine model of narcolepsy illustrate the importance of non-MHC genes in disease predisposition. In this model, narcolepsy is transmitted as a single autosomal recessive trait, canarc-1. In spite of an association with immune-related polymorphisms, narcolepsy does not appear to be a classic autoimmune disease. Other pathophysiologic models involving the microglia and the release of specific cytokines in the CNS may be involved and are being explored. This approach, together with positional cloning studies in humans and canines, should reveal the cause of narcolepsy and open new therapeutic avenues.

HLA class II haplotype and sequence analysis support a role for DQ in narcolepsy.

A systematic haplotype and sequencing analysis of the HLA-DR and -DQ region in patients with narcolepsy was performed. Five new (CA)n microsatellite markers were generated and positioned on the physical map across the HLA-DQB1-DQA1-DRB1 interval. Haplotypes for these new markers and the three HLA loci were established using somatic cell hybrids generated from patients. A four-marker haplotype surrounding the DQB1(*)0602 gene was found in all narcolepsy patients, and was identical to haplotypes observed on random chromosomes harboring the DQB1(*)0602 allele. Eighty-six kilobases of contiguous genomic sequence across the region did not reveal new genes, and analysis of this sequence for single nucleotide polymorphisms did not reveal sequence variation among DQB1(*)0602 chromosomes. These results are consistent with other studies, suggesting that the HLA-DQ genes themselves are among the predisposing factors in narcolepsy.

TNF2, a polymorphism of the tumour necrosis-alpha gene promoter, is a component of the celiac disease major histocompatibility complex haplotype.

Celiac disease (CD) is an immune disease triggered by the cereal antigen gliadin, resulting in villous atrophy in the small intestine. Susceptibility to the development of CD is strongly influenced by genes in the major histocompatibility complex, in particular alleles of the DQ genes in the class II region. However recent evidence has suggested that the major histocompatibility complex (MHC) class III region may be linked to celiac disease independently of the class II region. Among the genes located in this area is TNF-alpha, which encodes the cytokine tumor necrosis factor-alpha which has a broad range of pro-inflammatory, immunomodulatory and catabolic activities. Therefore, aberrant expression of TNF-alpha could be important in the pathogenesis of MHC-associated immune disorders. A TNF-alpha variant with a polymorphism in its promoter region has been described and designated TNF2. TNF2 has been associated with a variety of MHC-linked diseases, including systemic lupus erythematosus, dermatitis herpetiformis and insulin-dependent diabetes mellitus (IDDM), as well as parasitic infections. TNF2 has previously been shown to be associated with the MHC haplotype HLA A1-B8-DR3-DQ2, which confers susceptibility to CD. We have analyzed the distribution of TNF2 alleles in a group of celiac patients (n = 52) compared to controls (n = 52) in an effort to evaluate its role, if any, in susceptibility to the condition. TNF2 has a frequency of 0.5000 (SE +/- 0.0490) in CD, compared to 0.1635 (+/- 0.0362) in a control sample (p < 10(-6)). Of 52 patients, 44 carried one or more TNF2 alleles. Analysis indicates that the distribution of TNF2 is best explained by assuming 100% allelic association between it and HLA-DQB1*0201 (frequency = 0.7791 +/- 0.0447). However, the number of TNF2 heterozygotes significantly exceeds expectations and measurements of linkage disequilibrium confirm that allelic associations spanning the DQ and TNF regions are strongly maintained in CD. Taken together, these results indicate that TNF2 may have a role in the pathogenesis of CD; however, since it is not an independent association, the possibility that TNF2 constitutes a passive component of the CD haplotype cannot be excluded.

O09 - The natural history of a microsatellite located in the HLA DQ region

O09 - The natural history of a microsatellite located in the HLA DQ region

HLA-DQ gene polymorphism in primary IgA nephropathy in three European populations

MHC Class II genes may contribute to susceptibility to IgA nephropathy (IgAN). We have previously identified a restriction fragment length polymorphism (RFLP) of the DQB1 region that associated with IgAN in British Caucasoids. However, another group, while demonstrating a DQB1 association, was unable to confirm our finding. MHC molecules are heterodimers consisting of an alpha and beta chain, and thus polymorphism of the DQA1 alpha chain may also be important to disease pathogenesis in IgAN. Therefore, we have determined DQA1 alleles and re-examined DQB1 alleles in British Caucasoids with IgAN using an approach that can differentiate between the common DQ alleles; we have also extended our studies to Caucasoid populations from Northern and Southern Europe, thereby addressing the possibility of variation in genetic susceptibility between populations. DNA was prepared from IgAN patients (British, N = 105; Italian, N = 71; Finnish, N = 48) and healthy controls (British, N = 111; Italian, N = 63; Finnish, N = 41). DQA1 alleles were identified by TaqI RFLP and Southern blotting; alleles that could not be fully resolved by Taq Southern blotting were identified by PCR-RFLP. DQB1 alleles were identified by polymerase chain reaction (PCR) based technique (PCR-RFLP). No consistent association of DQ alleles were found between the populations studied. In British patients a decreased frequency of DQB1*0201 was observed (P = 0.008), in Finnish patients a decreased frequency of DQB1*0602 was observed (P = 0.01), and in Italian patients no association between DQ markers and IgAn was found. These data demonstrate population variation in disease association, but no strong or consistent association in the DQ region.

Genetics of insulin-dependent diabetes mellitus.

IDDM is caused by autoimmune destruction of insulin-producing beta cells of the pancreas in genetically susceptible individuals. Although the incidence and prevalence if IDDM in Japan are much lower than those in Caucasian countries, the recurrence risk in siblings of IDDM probands is much higher than the population prevalence, indicating that IDDM is clustered in families even in Japan, where the incidence of the disease is the lowest in the world. The higher concordance rate in monozygotic twins than in dizygotic twins indicates that genetic factors contribute to the familial clustering of IDDM in Japan. Analysis of the HLA region revealed that susceptibility genes (IDDM1) consist of multiple components, those in class II DR and DQ regions and another in the class I region. Analysis in NOD mice, an animal model of IDDM, supports this observation: susceptibility genes (Idd1) are mapped to class II A and E regions, but the incidence of the disease is strongly affected by a gene or genes outside of this segment (Idd16). Studies in both humans and an animal model will clarify the genetic components of IDDM, facilitating prediction of the disease and the development of effective strategies for its prevention.

5.2#43 - Sequences in DQ AND DP regions are important for the expression of cutaneous leishmaniosis

5.2#43 - Sequences in DQ AND DP regions are important for the expression of cutaneous leishmaniosis

Vitiligo is associated with a significant increase in HLA-DR6 and a decrease in DQw2 antigens in Northern Italian patients

Background Pathogenesis of vitiligo is still unclear; although the mechanism of melanocyte destruction is not know, reports of abnormalities in immunoregulation and immune reactivity in these patients support the autoimmune theory of the disease. A wide variety of autoimmune disorders have been associated with HLA antigens, and at the present time there are conflicting results about the association between vitiligo and HLA phenotypes.Objective and methods To determine if some increases in certain HLA antigens in the Northern Italian population suffering from vitiligo exist, we studied 33 patients, and we compared the results obtained with those observed in 443 control subjects of the same geographical area.Results HLA-DR and DQ typing showed a statistically significant increase of DR6 antigen and a statistically significant decrease of DQw2 type. The comparison of the phenotype frequencies of the loci A,B and C observed in the patients and in the control group showed no statistically significant differences after the p correction.Conclusion This study showed that genes in or closely linked to the HLA-DR and DQ regions of the major histocompatibility complex could influence susceptibility to vitiligo in Northern Italian patients.

No association between HLA DQ and -DR genotypes with nasopharyngeal carcinoma in southern Chinese

The pathogenesis of nasopharyngeal carcinoma (NPC) is multifactorial. Associations have been reported between HLA and NPC. We studied the HLA-DR and -DQ regions on the molecular level in 136 persons (51 NPC patients and 85 healthy controls) from southern China, a particularly high-prevalence area for NPC. Restriction fragment-length polymorphism (RFLP) was used to genotype the MHC class II DRβ, DQα, and DQβ regions of the subjects. Polymerase chain reaction (PCR) using sequence-specific primer (SSP) for DQβ genes was also performed. By RFLP, no significant difference was observed with respect to DRB, DQA, and DQB genes. By PCR SSP typing, we confirmed that there was no significant difference between NPC patients and controls with respect to DQβ alleles. Our study suggests that HLA-DQ and -DR genes are not associated with NPC in southern Chinese and there may be other gene loci that predispose them to have such a high prevalence of the disease.

Lack of association between HLA-DQ and -DR genotypes and asthma in southern Chinese patients.

Asthma is an inflammatory disease with a strong genetic predisposition. We have studied a group of unrelated asthmatic patients of southern Chinese origin on their HLA-DR and -DQ regions using molecular techniques and compared them with 104 healthy controls of the same ethnic origin. Restriction fragment length polymorphism (RFLP) was used to genotype the MHC class II DR beta, DQ alpha and DQ beta loci of the subjects. Polymerase chain reaction (PCR) using sequence specific primer (SSP) for DQ beta genes was also performed. No significant difference was found in the HLA-DQ and -DR loci between the patients and the controls. All patients had their serum IgE antibody levels measured, bronchial reactivity assessed by histamine broncho-provocation and cutaneous reactivity to common allergens determined by skin-prick tests to Dermatophagoides pteronyssinus, Dermatophagoides farinae, mixed grass pollens, Aspergillus fumigatus, cat fur and dog dander and they were classified respectively. The HLA-DR and -DQ genotypes of these subgroups of patients were compared. There was no significant difference among these subgroups of patients according to their serum IgE levels, the degree of bronchial reactivity and whether they were positive for the skin tests for the various allergens respectively. The results suggest that HLA-DQ and -DR genotypes are not associated with asthma in southern Chinese people.

Progression of HIV infection is associated with HLA-DQ antigens in Caucasians and African Americans.

In our previous work with human leukocyte antigen (HLA) association in human immunodeficiency virus (HIV) infection, African Americans (Afr Ams) and Caucasians (Caucs) exhibited HLA markers that were associated with protection or disease. The present study was designed to establish if HLAs were associated with the severity of HIV infection and progression to AIDS in Afr Am and Cauc adults. The frequency of serologically determined antigens (Ags) in the regional control population was compared to the HIV-infected population and the HIV-infected slow progressors were compared to rapid progressors by race. chi 2 analysis with Bonferroni adjustment, Kaplan-Meier survival analysis, linear logistic regression, Cox model of proportional hazards and standardized deltas were applied as applicable. Immune parameters were monitored over a mean follow-up period of 23 +/- 2 months for Afr Ams (n = 35) and 25 +/- 5 months for Caucs (n = 24). A better prognosis in the HIV+Afr Am group was associated with HLA-DQ1 with a risk ratio of 0.295. In the HIV+Cauc group, a preferable prognosis was associated with HLA-DQ3 with a risk ratio of 0.11, and a poor prognosis was associated with HLA-DQ2 with a risk ratio of 7. Afr Am haplotypes that appeared to have the greatest association with rapid progression of HIV infection were A69(28)-B40 and related haplotypes as well as B12-DR14(6). Cauc haplotypes with the strongest association with rapid and slow progression of HIV infection were A28-B17-DR9 and A30(19)-B67, respectively. The DR Ags of at least one haplotype that led to rapid progression in both races were associated with DQ9(3). An 'immune response' gene (DQ region) may control the progression of HIV infection in adults. The rapidly progressive DQ-associated peptide might block the progression of HIV if given as a novel vaccine.

Molecular genetics of MHC class II alleles in Chinese patients with IgA nephropathy

We have studied the restriction fragment length polymorphism (RFLP) of the major histocompatibility complex (MHC) class II DQ and DR regions of 79 Chinese patients with IgA nephropathy (IgAN) and compared it with 104 normal Chinese controls. The DR and DQ alleles were confirmed by polymerase chain reaction using sequence specific primers. There was a significantly higher frequency of homozygous DQ beta 3b (DQ7) in patients with IgAN (16.4%) compared with controls (5.7%). Seventy-one IgAN patients had their renal biopsies graded according to histopathological severity: grades I, II or III. There was no statistical difference in the DR and DQ alleles among the three grades. Seventy-three patients were classified into group A with normal and stable renal function (serum creatinine < or = 150 mumol/liter) and group B with chronic renal failure (serum creatinine > 150 mumol/liter). There was a significant increase in frequency of DQA2 U (DX alpha U) allele in group B (66.9%) compared with group A (26.9%). Also, there was an increased frequency of DQ alpha 2 allele in the group A (40.4%) compared with group B (14.3%). Out of the 24 patients carrying the DQ alpha 2 allele, 17 were DQA2 U allele-negative and they all had normal renal function, suggesting that DQA2 U allele is associated with a poor prognostic factor in IgAN. The study shows that DQ alleles are probably the important genetic loci or are close markers for the disease susceptibility and prognostic index for IgAN in Chinese people.

Both DQB genes are expressed in BoLA haplotypes carrying a duplicated DQ region.

The objective of this study was to determine whether more than one DQB gene is expressed in three BoLA haplotypes that have a duplicated DQ region. Leukocyte mRNA from three animals genotyped at the BoLA-A, DQB, and DRB3 loci was used as template for reverse transcription-polymerase chain reaction (RT-PCR), cloning, and DNA sequencing. Five DQB alleles were identified. All cDNA clones were 564 base pairs (bp) in length, including 507 bp of nonprimer-derived sequence that contained the coding sequence for the full length of exon 2 and 74 amino acids of exon 3. Three alleles were assigned to the DQB1 locus and two were assigned to DQB2 on the basis of sequence comparisons with previously reported alleles. The expression of DQB1 and DQB2 in individual animals was examined by RT-PCR followed by double digestion of the 564 bp PCR products with Eco O109 I and Dra III in order to discriminate the DQB alleles. Evidence that DQB1 and DQB2 are both transcribed was obtained for three different BoLA haplotypes with DQB duplications, DQB10, DQB11C, and DQB12. These results suggest that the duplication or deletion event that gave rise to the DQB1 and DQB2 genes is a relatively recent event in the evolution of the cattle MHC.

Genomic MHC haplotyping of mutant cell lines using a novel marker.

The aim of this study was to characterize MHC mutant cell lines by studying haplospecific markers within the MHC and specifically in the 250 kilobase (kb) region between the HLA B and TNF loci. This region has been difficult to define because of the lack of appropriate markers. Spontaneous MHC mutants were isolated after immunoselection with an anti-HLA A2 monoclonal antibody and complement. Ten mutants were characterized using serological or allelic and genomic DNA markers within the HLA A to HLA DQ region of the MHC. Most mutants lost at least the 3 megabases of DNA from HLA A to HLA DQ viz the whole haplotype carrying HLA A2. Variants which have lost either HlA A alone or HLA A and HLA B were also found. The results show that it is possible to map the extent of the deletion between HLA B and TNF. Haplospecific scanning patterns for the CL region appear particularly useful.

MHC class II haplotypes and linkage disequilibrium in primates

The loci encoding the major histocompatibility class II cell surface antigens DR, DQ, and DP exhibit a remarkable degree of allelic polymorphism. Strong linkage disequilibrium is also found between these loci in the human population. To study the evolutionary conservation of this disequilibrium the DQA1, DQB1, and DRB1-6 loci were analyzed in chimpanzee and gorilla by sequencing or/and oligonucleotide hybridization of PCR-amplified DNA. This analysis revealed several new DRB sequences. The distribution of DRB loci differs between human and nonhuman primate haplotypes, and the strong disequilibrium found on human haplotypes between alleles at DQA1 and DQB1 as well as between the DQ loci and the DRB1 locus was not detected in the nonhuman hominoids. Extensive recombination within and between the DR and DQ region appears to have occurred during the 3–7 million years since the divergence of the three species, resulting in little similarity of haplotypes between species. The strong disequilibrium found in the human species between these loci may either reflect haplotype-specific barriers to recombination, recent founder effects in the evolution of humans, or selection for specific haplotypes.

HLA-DQA1, DQB1 and DPB1 alleles on HLA-DQ2- and DQ9-carrying extended haplotypes.

DQA1, DQB1 and DPB1 alleles were investigated in a large panel of samples carrying HLA-DQ2- and HLA-DQ9-bearing extended haplotypes. Every instance of the [HLA-B8, SCO1, DR3, DQ2a] and [HLA-B18, F1C30, DR3, DQ2b] extended haplotypes carried the DQA1*0501 allele, while every instance of [HLA-B44, FC31, DR7, DQ2c], [HLA-B47, FC91,0, DR7, DQ2c] and [HLA-B57, SC61, DR7, DQ2d] carried the DQA1*0201 allele. All HLA-DR3, DQ2 and HLA-DR7, DQ2 extended haplotypes carried the DQB1*0201 allele. Every example of [HLA-B57, SC61, DR7, DQ9] carried the DQB1*0303 allele. Several associations between the DPB1 alleles and some HLA-DQ2- and DQ9-carrying extended haplotypes were identified. HLA-DPw2-encoding alleles, DPB1*0202 (50%, p < 0.001) and 0201 (30%), were found on the [HLA-B18, F1C30, DR3, DQ2b] extended haplotype. Every instance of the [HLA-B57, SC61, DR7, DQ9] extended haplotype carried the DPB1*0401 allele. Also, we have confirmed the associations of the DPB1*0101 and DPB1*0401 alleles with the [HLA-B8, SC01, DR3, DQ2a] extended haplotype. The analysis of homozygous typing cells carrying the [HLA-B44, FC31, DR7, DQ2c] extended haplotype showed that the DPB1*0401 and 0201 alleles were present at similar frequencies (37.5%), while the DPB1*1101 allele was found in only 25% of these haplotypes analyzed. Our results suggest that the constancy of the DNA of the HLA-B, DR, DQ regions may extend to the DP region and that the extent of such fixity varies, perhaps as the result of ethnic variability of the population studied.

Electrophoretic mobility polymorphisms of DR and DQ region PCR fragments simplify sequencing efforts for allele and haplotype assignment

Electrophoretic mobility polymorphisms of DR and DQ region PCR fragments simplify sequencing efforts for allele and haplotype assignment

Increasing complexity of HLA-DR2 as detected by serology and oligonucleotide typing

Serological and obligonucleotide typing was performed on a number of HLA-DR2-positive cells from different ethnic origin, including DR2 haplotypes with various DQ associations. Exons 2 of DRB1 and DRB5 of DR2-positive individuals were locus-specific amplified and hybridized with a number of different oligonucleotides capable of discriminating between the various Dw2, Dw12, Dw21, and Dw22 associated sequences. The linkage of DRB with DQA1 and DQB1 in these haplotypes was analyzed. Among the DR2-positive cells we could define 10 different DR DQ haplotypes by serology and 13 by oligonucleotide typing. The DR2.ES specificity is a serological DRw15 variant which could not be discriminated by oligonucleotide typing from a DRw15 DQw5 haplotype. The DR2.JA variant represents a unique DRB1∗1602 DRB5∗0101 haplotype. The DR1+2s haplotype consists of a DRB1 DQ region from a Dw1 and a DRB5 gene from a Dw2 haplotype. Its short DR2 serum pattern can be explained by the absence of a DR2 DRB1 gene product. DRB5∗0101 sequences were found in association with DRB1∗1501, ∗1502, ∗1602, and ∗0101 alleles. Since the DRB5 gene is capable of such different associations it is comparable to the DRB3 and DRB4 genes. This may have implications for the definition of the broad DRB5 gene product. New DR2 haplotypes included the following DQ combinations: DQw2-positive DQA1/B1∗0301/0201 and DQw6-positive DQA1/B1∗0102/0601 and ∗0102/0603 haplotypes.

HLA and IDDM: Facts and speculations on the disease gene and its mode of inheritance

1. The mode of inheritance of the DR3- and DR4-associated susceptibility genotype is essentially recessive, based on both the segregation data and the existence of Hardy-Weinberg equilibrium in Ashkenazi Jewish and possibly in patients of other populations. 2. Maternal effects may alter the expressivity of IDDM in some susceptible offspring, depending on the maternal DR genotype. Thus, the number of susceptible DR4 types inherited from the mothers may be decreased in certain population samples. Conceivably, these maternal effects also account for the smaller proportion of diabetic children born to diabetic women than to diabetic men. Conversely, maternal DRw6 may raise this risk. 3. The locus of the susceptibility gene is most likely in the DQ region. While specific DQA1 and DQB1 alleles are very closely associated with IDDM in some populations, neither is completely associated with it in DR4 haplotypes and neither accounts for the differences in IDDM susceptibility associated with DR3 haplotypes. 4. Linkage disequilibrium between DR and DP alleles in affected haplotypes indicates the existence of subsets of DR3 and DR7, which account for all or most of the risk to those haplotypes. The possibility of direct DP effects is less likely because the respective DP alleles are different and because DR4 does not maintain disequilibrium with DP alleles in either affected or unaffected haplotypes. 5. The DQA2-BglII-7.2Kb polymorphism in complete association with affected B8,DR3 haplotypes suggests the possible involvement of DQA2.(ABSTRACT TRUNCATED AT 250 WORDS)