DQB1 promoter sequence variability and linkage in caucasoids

Sequence variations in the transcriptional regulatory region and intron1 of HLA-DQB1 gene and their linkage in southern Chinese ethnic groups

Sequence polymorphism in the transcriptional regulatory region extending to intron1 (DQRRI1) of HLA-DQB1 gene, and their haplotypic distributions were investigated in southern Chinese populations. We cloned and sequenced a 1.1-kb segment containing the transcriptional regulatory region, exon1, and partial intron1 of HLA-DQB1 gene of 37 individuals from nine different ethnic groups in southern China. A high-density map of 162 polymorphisms, including 152 single nucleotide polymorphisms (SNPs) and 10 insertion-deletion polymorphisms, was revealed. By comparing these data with SNPs deposited in dbSNP database in National Center for Biotechnology Information and polymorphisms that have been reported, 66 polymorphisms were firstly reported. A total of 16 different haplotypes were detected based on these 162 polymorphisms. The distribution of 16 alleles of DQRRI1 as well as their linkage with DQB1 exon2 alleles was also investigated based on the population study and phylogenetic analysis. Tight linkage between these two regions were discovered, as each of DQB1*02, DQB1*03, DQB1*04, DQB1*05, and DQB1*06 alleles was seen to be linked with specific DQRRI1 allele. Our study showed different pattern of transcriptional regulatory region, exon1, and intron1 of different DQB1 alleles.

Allele-specific quantification of HLA-DQB1 gene expression by real-time reverse transcriptase-polymerase chain reaction

In addition to coding region polymorphism, allele-specific variation in the upstream regulatory region of the HLA-DQB1 gene has been detected. Reporter gene assays and transfection studies have indicated that HLA-DQB1 promoter polymorphism may be of functional significance. The aim of this study was to utilize real-time reverse transcriptase-polymerase chain reaction (RT-PCR) for allele-specific quantification of HLA-DQB1 expression and to analyze cell-specific HLA-DQB1 expression in vivo. For the allele-specific quantification of DQB1 gene products, a real-time RT-PCR set of primer pairs (n=27) and probes (n=5) targeting exon 2 variability was established. The robustness and integrity of the assay system were confirmed by using recombinant DQB1 exon 2 plasmid clones as active exogenous controls. Sensitivity and reproducibility were assessed by serial dilution and allelic mixing analyses. In application to the study of allele-specific expression of DQB1 gene products during cytokine-driven maturation of monocyte-derived dendritic cells, differential patterns of allelic expression in heterozygous individuals were observed for DQB1*0301, compared to DQB1*0501 and DQB1*0602. At maximum, 1.9-fold (*0301/*0501) and 2.5-fold (*0301/*0602) higher induction was seen for DQB*0301. In conclusion, HLA-DQB1 expression can be analyzed by real-time RT-PCR suitable for cell- and allele-specific detection of HLA-DQB1 transcripts in homo- and heterozygous combinations.

The HLA-DRB, -DQB polymorphism and anti-insulin antibody response in Slovenian patients with type 1 diabetes

A combination of specific HLA class II antigens and the presence of type 1 diabetes (T1D)-related antibodies has a high positive predictive value for T1D but low sensitivity. The aim of the present study was to determine the frequencies of HLA-DRB-DQB deduced haplotypes associated with susceptibility and protection in Slovenian patients with established T1D, to evaluate the relationship between the HLA-DRB1-QBP-DQB1 haplotypes and the presence of insulin autoantibodies (IAA) and glutamic acid decarboxylase antibodies (GADA), and to access the possible impact of polymorphic QBP promoters on this relationship. A cohort of 135 patients with T1D (age 17.5 +/- 7.0 years, duration of T1D 9.14 +/- 6.3 years) was investigated. HLA-DRB1 and DQB1 alleles were typed using the polymerase chain reaction (PCR)-reverse line blot method. QBP promoter region alleles were determined using PCR-sequence-specific oligonucleotide hybridization (SSO) and PCR-sequence-specific primers (SSP). IAA and GADA antibodies were determined by enzyme-linked immunosorbent assay (ELISA). The chi-square test with Yates' correction was used for statistical analysis. Deduced haplotypes DRB1*0301-DQB1*0201 (P = 0.0001, OR = 3.4), DRB1*0401-DQB1*0302 (P = 0.0001, OR = 29.8), and DRB1*0402-DQB1*0302 (P = 0.008, OR = 4.7) were significantly more common, and DRB1*1501-DQB1*0602 (P = 0.0001, OR = 0.03) significantly less common in the investigated cohort than in a Slovenian control group. The highest risk and the strongest protective HLA-DR-DQ haplotypes found in Slovenian patients with T1D did not differ from those found in other Caucasian populations. While the DRB1*0301-QBP2.1-DQB1*0201 haplotype, where QBP2.1 did not help to further distinguish DQB1*0201-possessing haplotypes in IAA-positive and IAA-negative patients, was strongly associated with the presence of IAA, the DRB1*0101-QBP5.12-DQB1*0501 haplotype, although not protective compared to the control population, was associated with an absence of IAA in the investigated cohort. It is suggested that there may be a combined influence of the QBP5.12 promoter and the DQB1*0501 functional molecule on reduced IAA production.

Relative quantification of HLA-DRA1 and -DQA1 expression by real-time reverse transcriptase-polymerase chain reaction (RT-PCR)

Polymorphism in the upstream regulatory region (URR) of the MHC class II DQA1 gene defines 10 different alleles named QAP (DQA1 promoter). In vitro studies have suggested that allelic polymorphism in the HLA-DQA promoter region may result in differences in HLA-DQA1 gene expression. In the present study, we used real-time reverse transcriptase-polymerase chain reaction (RT-PCR) to quantify differences in HLA-DQA1 gene expression. After the isolation of total mRNA, reverse transcription into cDNA was carried out using random hexamer priming and moloney murine leukaemia virus (MMLV) reverse transcriptase. Quantification of DQA1 mRNA species using a set of six group-specific primer pairs for the detection of HLA-DQA1*01, *02, *03, *04, *05 and *06 was carried out on an ABI PRISM GeneAmp 7700 Sequence Detection System (Perkin Elmer, Foster City, CA) with real-time detection and quantification taking advantage of the fluorescence TaqMan technology (Perkin Elmer, Foster City, CA). Normalization of cDNA templates was achieved by glyceraldehyde-3-phosphate dehydrogenase (GAPDH) quantification. In addition, the total amount of mRNA produced by HLA-DQA1 and HLA-DRA1 expression was quantified for comparison. Subsequently, this approach was validated using Raji and HUT-78 cell lines and tested with peripheral mononuclear cells (PBMC) of 45 samples taken from healthy volunteers. The sensitivity was determined with > or = 10(2) copies. Comparison of the allele-specific DQA1 expression with the total expression of DQA1 and DRA1 mRNA indicated that DQA1*04 expression was increased compared with the expression of other alleles of the DQA1 gene. Thus, allele-specific quantification of DQA1 gene products could be achieved by real-time RT-PCR suitable for the analysis of differential expression of DQA1 mRNAs in homozygote and heterozygote combinations.

DQA1 and DQB1 promoter diversity and linkage disequilibrium with class II haplotypes in Mexican Mestizo population

The upstream sequences in the 5' flanking region of HLA class II genes, regulate their expression and contribute to the development of immunological diseases. We analyzed 105 healthy unrelated Mexican Mestizos for QAP and QBP polymorphism. DNA typing for DRB1, DQA1, DQB1, QAP1 and QBP1 was done using a standardized PCR-SSOP. Although all QAP alleles previously described were found in Mexicans, the distribution differed as compared to other populations. QAP-3.1, 4.1 and 4.2 were the most frequent alleles and were associated with DQA1*03, *0501 and *0402 respectively. The prevalent QBP alleles were 3.21, 3.1 and 4.1 found mainly associated with DQB1*0302, *0301 and *0501. Linkage disequilibria between the promoter and the corresponding DQA1 and DQB1 allele, are in general the same as described by others. A total of 61 different haplotypes were defined, only six of them with a frequency above 4%. The haplotypes DRB1*0407-QAP-3.1-DQA1*03-QBP-3.21-DQB1*0302 (HF = 14.37%) and DRB1*0802-QAP-4.2-DQA1*0401-QBP-4.1-DQB1*0402 (HF = 14.22%), which have an Amerindian ancestry, are the most frequent in Mexicans. Some rare combinations were detected such as DRB1*0405-QAP-1.3-DQA1*0101/4-QBP-5.11/5.12-DQB1*0501 and DRB1*0403-QAP-3.2-DQA1*03-QBP-3.21-DQB1*0302, probably due to ancient recombination events. This knowledge is relevant as a basis to evaluate functional implications and to explore the role of promoter diversity in disease expression.

Extensive HLA class II studies in 58 non-DRB1*15 (DR2) narcoleptic patients with cataplexy

Narcolepsy is a sleep disorder that has been shown to be tightly associated with HLA DR15 (DR2). In this study, 58 non-DR15 patients with narcolepsy-cataplexy were typed at the HLA DRB1, DQA1 and DQB1 loci. Subjects included both sporadic cases and narcoleptic probands from multiplex families. Additional markers studied in the class II region were the promoters of the DQA1 and DQB1 genes, two CA repeat polymorphisms (DQCAR and DQCARII) located between the DQA1 and DQB1 genes, three CA repeat markers (G51152, T16CAR and G411624R) located between DQB1 and DQB3 and polymorphisms at the DQB2 locus. Twenty-one (36%) of these 58 non-DR15 narcoleptic patients were DQA1*0102 and DQB1*0602, a DQ1 subtype normally associated with DRB1*15 in DR2-positive narcoleptic subjects. Additional microsatellite and DQA1 promoter diversity was found in some of these non-DR15 but DQB1*0602-positive haplotypes but the known allele specific codons of DQA1*0102 and DQB1*0602 were maintained in all 21 cases. The 37 non-DQA1*0102/DQB1*0602 subjects did not share any particular HLA DR or DQ alleles. We conclude that HLA DQA1*0102 and DQB1*0602 are the most likely primary candidate susceptibility genes for narcolepsy in the HLA class II region.