Generic HLA-DRB1 gene oligotyping by a nonradioactive reverse dot-blot methodology

Synergistic effect of two HLA heterodimers in the susceptibility to celiac disease in Tunisia

The DR and DQ HLA genotypes of 94 Tunisian children affected with celiac disease are analyzed so that we can gain a better understanding of the HLA component of this disease. All of them carry at least one of two specific heterodimers: a DQ heterodimer, encoded by DQA1*0501, DQB1*0201 and/or a DR heterodimer, encoded by the nonpolymorphic gene DRA and the DRB4 gene. Quantifying the relative penetrances of all susceptible genotypes gives evidence for a synergistic effect of these two heterodimers and for a dose effect of the alleles encoding the beta chains of these two heterodimers. The DR3DR7 individuals have the greatest risk. They present the two kinds of heterodimers and carry two DQB1*0201 alleles. Celiac disease is the first HLA-associated disease for which the at-risk genotypes are so well delineated.

Susceptibility to coeliac disease in Tunisian children and GM immunoglobulin allotypes

Coeliac disease is a malabsorption disorder of the small intestine resulting from ingestion of gluten. The immunogenetic component is clearly demonstrated by the association of the disease with human leukocyte antigens (HLA). Among other candidate genes are the GM allotypes, which are the markers of the constant parts of heavy chains of the subclasses IgG1, IgG2 and IgG3. GM immunoglobulin allotypes have been analysed in 131 unrelated Tunisian children with coeliac disease. All patients and their parents were tested for G1M(1, 2, 3, 17), G2M(23) and G3M(5, 6, 10, 11, 13, 14, 15, 16, 21, 24, 28) by the classical haemagglutination method. Genotypes and haplotypes were deduced from phenotypes in patients and their parents. Transmission disequilibrium tests were performed in 79 informative families. The GM*3;..;5* haplotype was transmitted more often (23) than not (8) by heterozygous parents (chi 2 = 7.26; P = 0.007). This difference remained significant after correction for multiple testing. This study provides evidence for association and linkage between GM and coeliac disease. It suggests that GM or genes close to GM play a role in the development of the disease.

Lack of correlation between genotype and phenotype in celiac disease

BACKGROUND

Celiac disease has a wide range of clinical features. The goal of this study was to evaluate whether specific HLA genotypes are associated with particular clinical appearances.

METHODS

One hundred forty-five patients with confirmed celiac disease were oligotyped for DR and DQ HLA genes. Clinical notes, physical examination, and a questionnaire provided their personal data. Patients were grouped into nine genotypic categories, according to the presence of the specific DQ heterodimer DQA1*0501-DQB1*0201 (hence termed alpha0beta0), in single or double dose, and the presence of the DRB4 antigen.

RESULTS

Age at first symptoms and age at beginning of gluten-free diet were not significantly different in the nine groups. The initial symptoms of the disease had a similar distribution in all groups. In twenty-seven patients, disease was diagnosed by family screening: they shared a similar HLA genotype with those who had relevant symptoms. The actual growth status-evaluated by standardized height, percentage of median weight for age, and percentage of median weight for height--was not different in the nine groups. Presence of unusual health complaints was not associated with a specific genotype.

CONCLUSIONS

There is no evidence that clinical features of celiac disease are associated with different HLA genotypes. Genes outside the HLA may play a relevant role.

Polymorphism of the HLA-DMA and DMB genes in rheumatoid arthritis

OBJECTIVE

To determine whether the HLA-DMA and DMB genes, whose encoded molecules are involved in HLA class II-restricted antigen presentation, contribute to the genetic susceptibility to rheumatoid arthritis (RA).

METHODS

One hundred ninety-one RA patients, 147 control subjects, and 218 HLA-DRB1 genotype-matched control subjects were oligotyped for DMA and DMB genes.

RESULTS

DMA*0103 and DMB*0104 were significantly increased in the RA patients compared with the randomly selected and the matched controls, thus indicating a direct influence of the DM genes. After stratification of the patients and matched controls according to DRB1 genotypes, only DMA*0103 was increased in the RA patients with DRB1*01, as well as in the patients negative for the RA-susceptibility DR alleles.

CONCLUSION

Our results suggest that DMA*0103 could play an additional role in the genetic susceptibility to RA.

Quantitative analysis of the usage of human T cell receptor alpha and beta chain variable regions by reverse dot blot hybridization

We previously developed an adaptor ligation-mediated PCR method to amplify the T cell receptor (TCR) cDNA pools. In the present study we applied reverse dot blot hybridization to PCR-amplified specimens for quantitative analysis of the usage of TCR alpha and beta chain variable (V) region. 44 VA sequence-specific oligonucleotide probes (SSOPs) and 38 VB SSOPs were synthesized corresponding to unique sequences of VA and VB subfamilies. Peripheral blood lymphocytes of ten healthy donors and five T cell clones established from bone marrow cells were examined for VA and VB usage using this method. The results were consistent with those obtained by a colony hybridization method and those by immunofluorescence staining using monoclonal antibodies to VA and VB. Thus, reverse dot blot hybridization for TCR V(alpha) and Vbeta is a new, easy and dependable technique useful for analysis of VA and VB usage by human T cells.

A computerized method to predict the discriminatory properties for class II sequencing based typing

Accurate identification of alleles or groups of alleles is obtained using DNA techniques for HLA class II typing. In PCR-SSP and PCR-SSO the typing resolution is dependent on the location of the amplification primers and the number of oligonucleotide probes used for hybridization. These primers are developed based upon the known allele sequences. However, the number of published allele sequences increases rapidly. Periodic reconsideration of the discriminatory properties of the methods used is necessary and often leads to the addition of primers, and an increase of ambiguous genotypes. SBT is a high-resolution class II typing method which utilizes the second exon sequence at all positions for typing. Using a generic amplification and sequencing approach, a limited number of ambiguous heterozygotes can be expected. However, the number of ambiguities is dependent on the location of the primers. These ambiguities can be solved by the use of group-specific primers in either the amplification or sequencing reaction. To identify the applicability of a SBT approach with respect to typing resolution, it is important to identify these ambiguities and develop strategies to solve them. We developed software that predicts the ambiguous heterozygotes, and analyzes their sequences for group specific primers, solving these ambiguities. The location of the primers is considered as well as the use of generic vs group-specific amplification or sequencing reactions. Allele sequences of all class II genes, as accepted by the WHO nomenclature committee for factors of the HLA system and submitted to the EMBL/Genbank databases, are analyzed to define the allelic discrimination level of HLA-DQB1, -DQA1, -DFB1, -DPA1, -DRB1, -DRB3, -DRB4, and -DRB5.

An evaluation of a multicenter study on HLA-DPB1 typing using solid-phase Taq-cycle sequencing chemistry

In HLA Class II genes, polymorphism is mainly located in the second exon. Most DNA based typing methods are confined to the identification of specific sequence motifs in the second exon. In contrast, Sequencing Based Typing (SBT) elucidates the entire exon 2 sequence for typing. Comparison of the obtained exon 2 sequence with an allele sequence library results in allele assignment. We tested the applicability of SBT using a protocol for amplification followed by solid phase Taq-cycle sequencing for HLA-DPB1 typing. A panel of 32 samples were typed by SBT at five test sites which are participating in the Sequencing Based Typing component of the 12th International Histocompatibility Workshop. The panel represents the existing polymorphism at all known polymorphic positions of exon 2, both in homozygous and heterozygous combinations. In this multicenter study we focused on the reliability of analyzing heterozygous sequences for HLA typing. A multi-sequence analysis approach, Polall, was developed to evaluate sequences obtained. The assignment of homozygosity and heterozygosity was validated by cluster analysis of chromatographic data of all sequences. Sequence characteristics were examined and considered for appropriate assignment. Differences in sequence characteristics that occurred between the test sites are considered in detail. The evaluation of data of 5 test sites reveals that Taq-cycle sequencing can reliably be performed for HLA-DPB1 SBT.

Immunogenetic study of couples with recurrent spontaneous abortions

OBJECTIVES

Clinical observations suggest that genetic and immunologic disparity could be a factor in fecundity. The HLA system (HLA) is polymorphic and TLX (Trophoblast Lymphocyte Cross-Reactive), which is also polymorphic, seems to be linked to it. The immunologic hypothesis follows that excessive HLA and TLX-sharing could explain the rejection of a semi-allogenic blastocyst. Study objectives are therefore twofold; To determine whether or not there is significant HLA-sharing between spouses with unexplained recurrent spontaneous abortions (RSA) and to determine whether or not there is an association between some HLA specificities and RSA.

STUDY DESIGN

The study includes only Caucasian couples that have had three successive spontaneous abortions. These were distributed in two groups: Group E: 18 couples either with known aetiology or with secondary RSA; Group U: seven couples with unexplained primary RSA; Control group C: 21 couples with at least two children and no spontaneous abortions. Tissue typing for HLA-A and B molecules was performed using serotyping methodology based on lymphocytotoxicity reaction. The different DRB1 alleles (class II) were determined by oligotyping with a non-radioactive reverse dot-blot methodology.

RESULTS

Statistical comparison shows that the number of couples without shared specificity is not significantly different between the three groups for each locus independently and for the set of three. Our results show also that the allelic frequencies are not significantly different between the three groups.

CONCLUSIONS

There is no higher HLA-sharing in couples with RSA than in fertile couples. Similarly, no particular HLA specificity can be associated with the RSA.

Analysis of the population of human T cell receptor gamma and delta chain variable region subfamilies by reverse dot blot hybridization

We have developed a simple method to analyze the population of T cell receptor (TCR) gamma and delta chain variable (V) region subfamilies by the application of reverse dot blot hybridization, which was originally developed for the analysis of human HLA-DR polymorphism. The four oligonucleotides corresponding to each TCR-gamma V region subfamily and the six oligonucleotides to each TCR-delta V region gene were synthesized, and tailed with dTTP. The cDNA was amplified by ligation-mediated PCR in the presence of biotinylated deoxynucleotides. Hybridization between immobilized specific oligoprobes and biotinylated target DNA was nonradioactively detected by a reaction using alkaline phosphatase. The population of the V region subfamilies of TCR-gamma and -delta in PBL analyzed by reverse dot blot hybridization described here showed good correlations with the result of colony hybridization.