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PubMed1994

Interactions between staphylococcal superantigens and human T-cell clones are predominantly but not exclusively governed by their T-cell receptor V beta usage.

Staphylococcal exotoxins (SE) are potent mitogens for human and murine T cells. Extensive studies in mice have demonstrated strict correlations between T-cell responses to individual SE and TCR V beta expression. Studies examining the TCR V beta expression of SE-activated human peripheral blood T cells also suggest close correlations, whereas the data reported using human T-cell clones (TCC) are conflicting. We have determined the cDNA TCRB sequences of 52 different human TCC, expressing 35 different T-cell receptor V beta (TCRBV)-encoded sequences. The TCC were tested in proliferative assays using nine different SE. Most of these TCC express V beta s which have not been tested previously in studies examining interaction between TCC and SE. The SE stimulated a variable fraction (1/48-31/52) of the TCC. The ability of a given SE to stimulate TCC in many cases correlated with V beta expression, but several exceptions were found. With one possible exception, comparisons between deduced amino-acid sequences within the 'fourth hypervariable region' of the TCR beta chain and SE responsiveness did not reveal potential SE binding motifs. We conclude that the reactivity of T cells towards SE is governed mainly by their TCR V beta expression. However, the authors' results also suggest that the interaction between SE and human T cells may involve elements unidentified as yet which are in addition to the beta chain of the TCR.

Amino Acid Sequence↗
PubMed1990

Functional properties of HLA-DR-BON alleles associated with DQw5(w1) and with DQw7(w3): a family study.

Among the DR specificities undefined by serology, DR-BON is peculiar because RFLP cannot distinguish it from the well-defined allele DR1 even if the two specificities are very different functionally. The occurrence of two DR-BON-like alleles in the same family, one associated to the DQw5 split of DQw1 and the other associated to the DQw7 split of DQw3, enabled us to compare the properties of these alleles. The RFLP analysis showed a typical DR1-like picture for both alleles when probed with DR beta, but for one of the alleles the DQ beta probe gave a DQw7 pattern. Primary mixed lymphocyte cultures showed weak to moderate stimulation between cells from individuals identical for one haplotype and differing for the DR-blank haplotypes, but by test with cloned reagents we were not able to define differences between the two DR-blank molecules. Two-dimensional gel electrophoresis and spot-test with a probe covering the third hypervariable region of the DRB1 gene showed no difference between the two alleles. We thus think that the two DR alleles are identical and that the stimulation observed in primary cultures probably is caused by incompatibility for DQ and DP or class I.

Alleles↗
PubMed1991

Binding of IgG to B cell via HLA molecules.

Binding of immunoglobulins to major histocompatibility complex (MHC) molecules was demonstrated by two different assays: the binding of IgG to B cells by flow cytometry, and purified MHC antigens with an Elisa assay. Fc fragment from immune-complex binds to the Fc receptor on B lymphocytes. Here, Fab was also shown to bind to B cells. This binding was inhibited by specific human allo anti-HLA Class I and II sera directed at the polymorphic sites. Thus, in addition to the Fc receptor, MHC can also serve as a binding site for IgG. In an Elisa assay using purified antigens, IgG was shown to bind to HLA Class I and II molecules. Other proteins such as transferrin, human serum albumin, gelatin, etc., did not bind to the MHC proteins. Immunoglobulins bound to MHC molecules by sites on the Fab fragment independent of the hypervariable region. This was demonstrated by the retention of antibody activity even after binding of antibody (anti-lactoferrin) to MHC. The relative avidity between Fab and HLA Class I and II was 4-8 x 10(5) M-1.

B-Lymphocytes↗
PubMed1991

Dw14(DRB1*0404) is a Dw4-dependent risk factor for rheumatoid arthritis. Rethinking the "shared epitope" hypothesis.

HLA-DR4 has been shown to be associated with risk for developing rheumatoid arthritis (RA) in multiple populations and racial groups. The allelic variants of DR4 share the DR4 serologic specificity but differ by 1 to 3 amino acids in the third hypervariable region (positions 67 to 74) and at positions 57 and 86 of the DR beta 1 chain. We have examined DR4 variants in 61 DR4+ RA cases and 55 DR4+ healthy controls. Dw14 was not associated with RA risk in DR4 heterozygous (DR4,X) cases. Only 15% of DR4,X cases had the Dw14 allele compared with 28% of DR4,X controls. In homozygous (DR4,4) individuals who also expressed Dw4, however, Dw14 was associated with increased RA risk. Moreover, the relative risk for Dw4,Dw14 (16.1, p = 0.001) actually exceeded that of Dw4,Dw4 (2.2, p = ns). Thus Dw14 is not an independent risk factor for RA but is a synergistic risk factor for individuals who also have the Dw4 allele.

Alleles↗
PubMed1991

Polymorphism of HLA-DRw52-associated DRB1 genes as defined by sequence-specific oligonucleotide probe hybridization and sequencing.

We have used group-specific DNA amplification and sequence-specific oligonucleotide probe (SSOP) hybridization to study DRB1 sequence polymorphisms associated with DR3, DRw11(5), DRw12(5), DRw13(w6), DRw14(w6) and DRw8 alleles. Group-specific amplification of DRw52-associated DRB1 alleles was achieved using a 5' amplification primer designed to hybridize with a first hypervariable region (HVR) sequence common to all known alleles in this group, together with a 3' intron primer. Prospective SSOP typing of DR3, DRw11, DRw12, DRw13, DRw14 and DRw8 alleles was performed in 318 individuals, including 124 patients, 46 family members and 148 unrelated marrow donors. Among the 395 DRw52-associated DRB1 alleles tested in our study, a subtype corresponding to the previously defined alleles DRB1*0301-2 (DR3), DRB1*1101-4 (DR5), DRB1*1201-2 (DR5), DRB1*1301-5 (DRw6), DRB1*1401-2 and 1404 (DRw6), and DRB1*0801-4 (DRw8) could be assigned in all but 6 individuals (1.9%) tested. In addition to the 22 known alleles, we identified two new DRw6-associated alleles, DRB1*13.MW(1) and DRB1*14.GB(1). DRB1*13.MW typed serologically as DRw13 and was identical to DRB1*1301 except at codon 71 where AGG encodes arginine instead of GAG encoding glutamic acid. DRB1*14.GB represents a DRB1*1402 variant whose sequence at codon 86 encodes valine (GTG) instead of glycine (GGT). These results demonstrate that SSOP methods represent an efficient and precise approach for typing DRB1 alleles and for identifying potential novel variants previously unrecognized by conventional typing methods.

Alleles↗
PubMed1993

HLA-DR1 and rheumatoid arthritis in Israeli Jews: sequencing reveals that DRB1*0102 is the predominant HLA-DR1 subtype.

Rheumatoid arthritis (RA) is associated with the HLA-DR4 cellular subtypes Dw4 and Dw14 in Caucasians, with Dw15 in Japanese, and possibly with HLA-DR1 in Israeli Jews. Sequencing studies in Caucasians have shown that these molecules share a common amino acid sequence in the third hypervariable region of the DR molecule (AA 67-74: LLEQRRAA or LLEQKRAA), suggesting that this sequence is primarily associated with RA. An important argument in favor of this shared-epitope hypothesis has been the reported association between DR1 and RA in Israeli Jews. However, a later report did not confirm this association, and cellular typing showed that Israeli DR1 consists of three or more subtypes, suggesting that new subtypes might be present. Since no sequencing data on Israeli HLA-DR1 genes have been reported, we sequenced the first domain (AA 10-91) of the DRB1 gene in 12 DR1-positive Israeli RA patients, 5 healthy controls and a homozygous typing cell (HTC), defining the major Jewish cellular HLA-DR1 subtype. DRB1*0102 (DR1 Dw20) was found in 8 RA patients, 3 controls and the HTC "LVA". DRB1*0101 (DR1 Dw1) was found in 4 RA patients and 2 controls. No other DR1 subtypes were encountered. In all 20 DR1 haplotypes, the DRB1*0101 or 0102 allele was associated with DQA1*0101 and DQB1*0501, being identical to the Caucasian DR1 haplotypes. Thus, at the sequence level, we found no basis for the reported extensive cellular heterogeneity of DR1 in the Israeli population.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1993

Isoelectric focusing subtypes of HLA-A can be defined by oligonucleotide typing.

This study describes a simple and direct method for sequence-specific oligonucleotide probe (SSOP) typing of the A locus of HLA class I genes. Genomic DNA from a panel of over 200 cells which have been characterized by the methods of serology and isoelectric focusing (IEF) for the HLA class I antigens was used for locus-specific PCR amplification of HLA-A sequences. Dot blot hybridization of the amplified products was performed with 28 SSOPs derived from hypervariable regions in exon 2 and 3. Co-amplification of three alleles of HLA-H pseudogene in apparent linkage disequilibrium with HLA-A2 and A10 was observed but did not interfere with the typing of HLA-A alleles. Using short SSOPs (15 nucleotides each) in single temperature tetramethylammonium chloride (TMAC) hybridization and washing steps, 30 IEF-definable isotypes of HLA-A antigens could be unambiguously defined by their hybridization patterns. Moreover, comparison of the typing results with available nucleotide sequences of HLA-A alleles showed that the conditions used allowed faithful detection of single codon mismatches between probe and template. Thus, these alleles can be identified by their unique hybridization patterns generated by the SSOPs. Nucleotide sequence analysis of any new HLA-A allele will further permit its rapid and unambiguous characterization by SSOP typing.

Amino Acid Sequence↗
PubMed1993

Rapid DNA typing for class II HLA antigens: subtyping of DRw52-associated DRB1 alleles.

Serologic typing for MHC class II antigens is incapable of identifying important subtypes for certain DRB1 alleles and occasionally leads to errors of assignment, particularly with the DR antigens associated with DRw52. To simplify DNA typing of DRw52-associated DRB1 alleles, we have developed a new rapid method using PCR-RFLP. The PCR-RFLP method is based on allele-specific amplification followed by digestion of PCR-amplified DNA with restriction enzymes. Group-specific amplification of the second exon of DR3, DR5, DR6 and DR8 was achieved using a 5' primer specific for the first hypervariable region sequence common to all alleles in this group and generic 3' primers. Human genomic DNA was amplified in a Perkin-Elmer Thermocycler. The presence of a 265 bp fragment was confirmed by agarose gel electrophoresis. Restriction enzyme digestion using Rsa I followed by polyacrylamide gel electrophoresis gave a pattern unique for some alleles and placed the remainder in subgroups. Digestion of the PCR product with one or two of the following enzymes (Asp 700, Hae II, Mnl I, Mbo II, Ksp I and Hph I) permitted the identification of 21 of the 22 alleles. DRB1*1103 and DRB1*1104 are not distinguished by this method and can be distinguished by SSOP or by using a specific 3' primer. For some heterozygous combinations, additional primers are used to provide full subtyping. This method provides a rapid and less costly alternative to PCR-SSOP for DRw52 subtyping in the smaller laboratory as only one amplification is required (two primers) for the majority of samples.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1996

Different contribution of HLA-DR and -DQ genes in susceptibility and resistance to insulin-dependent diabetes mellitus (IDDM).

Previous studies have indicated that certain alleles of HLA-DR and -DQ genes were strongly associated with susceptibility and resistance to insulin-dependent diabetes mellitus (IDDM), and the role of DQ molecule in IDDM has been suggested. To further clarify the association of DQ alleles with IDDM, we determined the nucleotide sequences of full-length cDNA from 13 DQA1 alleles and 14 DQB1 alleles. The sequencing analysis revealed sequence polymorphisms outside the hypervariable region of DQ genes. We then analyzed the DQA1 and DQB1 polymorphisms along with that of DRB genes in 86 B-lymphoblastoid cell lines (B-LCLs) from various ethnic groups and in healthy unrelated Japanese and Norwegian individuals. The allelic and haplotypic distributions in each population revealed the characteristic haplotypic formation in the HLA class II region. HLA genes in 139 Japanese and 100 Norwegian IDDM patients were analyzed. DQB1*0301 was negatively associated with IDDM in both ethnic groups, irrespective of associated DRB1 and DQA1 alleles. In DQB1*0302 positive populations, which represented a positive association with IDDM in both ethnic groups, DRB1*0401, *0404, *0802 haplotypes increased in the patients, whereas DRB1*0406 haplotype decreased. Considering about the hierarchy in DRB1 alleles with IDDM susceptibility (DRB1*0401>*0404>*0403 in Norwegian and DRB1*0802>*0403>*0406 in Japanese), the genetic predisposition to IDDM is suggested to be defined by the combination of DR-associated susceptibility and DQ-associated susceptibility and by the DQ-associated resistance which is a dominant genetic trait.

Alleles↗
PubMed1996

MHC class II alleles and haplotypes in patients with pemphigus vulgaris from India.

Pemphigus vulgaris (PV) is a blistering disease of the skin and mucous membranes characterized by an autoantibody response against a keratinocyte adhesion molecule, desmoglein 3, causing acantholysis and blister formation. We compared high resolution MHC class II alleles and haplotype frequencies (HLA-DRB, DQA1 and DQB1) in 37 patients with PV to 89 haplotypes of normal relatives from New Delhi and Ahmedabad. We found that PV patients had significantly increased frequencies of DRB1*1404 (P < 0.0001), DQA1*0101 (P = 0.001), and DQB1*0503 (P < 0.0001). These associations were due to the increased frequencies of the haplotype HLA-DRB1*1404, DRB3*0202, DQA1*0101, DQB1*0503 in patients compared to control haplotypes (p < 0.0001). Also, patients from Ahmedabad had a significant increase in HLA-DQB1*0302 (p = 0.03). An identical amino acid sequence (Leu-Leu-Glu-Arg-Arg-Arg-Ala-Glu), in positions 67-74 of the beta domain of DRB alleles is restricted to some DR14 alleles. Therefore, there are three possible explanations for class II allele involvement in autoantibody in PV patients with class II haplotypes marked by HLA-DR14. First, the class II alleles could be markers for an unidentified susceptibility gene in linkage disequilibrium with them. Second, the primary association could be with DQB1*0503 and the association with HLA-DR14 alleles would be the result of linkage disequilibrium. Third, the HLA-DRB1 locus susceptibility could involve a specific amino acid sequence in the third hypervariable region shared by several HLA-DR14 alleles.

Alleles↗
PubMed1998

DQCAR microsatellite polymorphism and susceptibility to rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic inflammatory joint disease associated with HLA-DR genes that share a five amino acid sequence motif, QKRAA or QRRAA, from position 70 to 74 in the third hypervariable region of the DRbeta1 molecule. Since the associations between DRB1 genes and susceptibility to RA are incomplete, in this study we examined the CA repeat polymorphic marker DQCAR, located between DQA1 and DQB1 genes, alleles in 98 adult patients with seropositive RA and 100 normal healthy controls. The prevalence of the DQCAR 117 allele was significantly higher in RA patients as compared to normal controls. On the other hand, the frequency of DQCAR 99 was lower in patients than in normal subjects. Analysis of the data suggested that DRB1 genes sharing the QKRAA/QRRAA epitope have the primary association with disease susceptibility and DQCAR alleles do not provide an additional risk for the development of RA.

Adult↗
PubMed1998

D6S273 microsatellite polymorphism and susceptibility to rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronic articular inflammatory disease associated with HLA-DR genes that share a five amino acid sequence motif, QKRAA or QRRAA, from position 70 to 74 in the third hypervariable region of the DRB1 molecule. Since these associations between DRB1 genes and susceptibility to RA are incomplete, we examined the role of a CA repeat polymorphic microsatellite marker, D6S273, located between HSP70 and Bat2 genes in the class III region of MHC, in susceptibility to RA. Ninety-seven adult patients with seropositive RA and 100 normal healthy subjects were studied. Two D6S273 alleles (132 and 138) showed significant differences in their prevalence in RA patients as compared to normal controls; allele 132 was significantly higher in total patients and in DRB1 QKRAA/QRRAA epitope-positive patients, and allele 138 was significantly higher in QKRAA/QRRAA-negative patients. Analysis of data suggested that the association of D6S273 132 allele with RA was secondary to that of DRB1 genes. On the other hand, D6S273 138 allele showed primary association with RA susceptibility in QKRAA/QRRAA epitope-negative patients. The D6S273 138 allele thus provides an additional risk in RA susceptibility. The results in the present study therefore suggest that two regions in MHC, DRB1 and D6S273, contribute to susceptibility to RA.

Adult↗
PubMed2006

Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali), Australia and New Guinea.

The genetic polymorphism at the dog leucocyte antigen (DLA) class II loci DQA1, DQB1 and DRB1 was studied in a large genetically diverse population of feral and wild-type dogs from the large island nations of Indonesia (Bali), Australia and New Guinea (Bali street dog, dingo and New Guinea singing dog, respectively). Sequence-based typing (SBT) of the hypervariable region of DLA-DRB1, -DQA1 and -DQB1 alleles was used to determine genetic diversity. No new DQA1 alleles were recognized among the three dog populations, but five novel DLA-DRB1 and 2 novel DLA-DQB1 allele sequences were detected. Additional unknown alleles were postulated to exist in Bali street dogs, as indicated by the large percentage of individuals (15%-33%) that had indeterminate DRB1, DQA1 and DQB1 alleles by SBT. All three groups of dogs possessed alleles that were relatively uncommon in conventional purebreds. The New Guinea singing dog and dingo shared alleles that were not present in the Bali street dogs. These findings suggested that the dingo was more closely related to indigenous dogs from New Guinea. Feral dog populations, in particular large ones such as that of Bali, show genetic diversity that existed prior to phenotypic selection for breeds originating from their respective regions. This diversity needs to be identified and maintained in the face of progressive Westernization. These populations deserve further study as potential model populations for the evolution of major histocompatibility complex alleles, for the study of canine genetic diversity, for the development of dog breeds and for studies on the comigration of ancestral human and dog populations.

Alleles↗
PubMed1996

Three subtypes of the tet(M) gene identified in bacterial isolates from periodontal pockets.

The tet(M) genes were characterized from 84 isolates of 10 different bacterial species isolated from the periodontal pockets of 16 patients with periodontal disease. A 740 bp polymerase chain reaction product from the hypervariable region of the tet(M) structural gene was cleaved with the restriction enzymes AluI and HinfI. Three different restriction patterns were identified for each of the two enzymes. By DNA sequencing, using a direct solid-phase automated sequencing method, the isolates could be grouped into 3 different clusters of tet(M) subtypes. The internal DNA homology within each subtype was 98-100%; the homology between clusters was 89-94%. Two different subtypes were identified in 9 of 10 bacterial species, and the remaining species had 3 different subtypes. One of the subtypes (M3) was seen mainly in the anaerobic isolates. This subtype was different from all earlier sequenced structural tet(M) genes present in the Genbank. Most patients had two different subtypes of tet(M), and a third subtype was seen in the 3 patients who exhibited the greatest variety of tetracycline-resistant bacterial species. It appears that the presence of one subtype of the tet(M) gene within a patient or bacterial species does not prevent the acquisition of another subtype of the same gene. This study identified a new subtype of the tet(M) gene and grouped it into 3 distinct yet highly homologous genetic subtypes.

Bacterial Proteins↗
PubMed2006

Contrasting genetic structures across two hybrid zones of a tropical reef fish, Acanthochromis polyacanthus (Bleeker 1855).

Hybrid zones are natural laboratories offering insights into speciation processes. Narrow hybrid zones are less common in the sea than on land consistent with higher dispersal among marine populations. Acanthochromis polyacanthus is an unusual bony marine fish with philopatric dispersal that exists as allopatric stocks of white, bicoloured and black fish on the Great Barrier Reef (GBR). At two latitudes, different morphs coexist and hybridize at narrow contact zones. Sequence data from mitochondrial Hypervariable Region 1 revealed contrasting patterns of introgression across these zones. At the northern hybrid zone, a single clade of mitochondrial haplotypes was found in all white fish, hybrids and tens of kilometres into pure bicoloured stock. At the southern hybrid zone, there was no introgression of mitochondrial genes into black fish and hybrids shared the bicoloured haplotypes. Based on this asymmetry, we postulate that black fish from the southern GBR have experienced a selective sweep of their mitochondrial genome, which has resulted in almost total reproductive isolation.

Animals↗
PubMed1993

A flow-cytometric approach to quantitative estimation of platelet surface immunoglobulin G.

Flow cytometry (FC) was used to estimate platelet-surface IgG (PSIgG) by quantifying the fluorescence of platelets incubated with a fluorescein isothiocyanate (FITC)-labelled polyclonal goat anti-human IgG antibody or FITC-labelled non-immune goat IgG. Results were expressed as relative fluorescence intensity (RFI) defined as the ratio of specific fluorescence (mean fluorescence of platelets incubated with the FITC anti-IgG) over non-specific fluorescence (mean fluorescence of platelets incubated with FITC non-immune goat IgG). A normal range was formed by analysing platelets from 71 healthy subjects. Platelets from 16 patients with a firm clinical diagnosis of immune-mediated thrombocytopenia had a mean RFI significantly higher (p < 0.001) than the controls, whereas platelets from 9 patients thought to have non-immune thrombocytopenia had an RFI not significantly different from the normal controls. From a prospectively studied group of 62 patients with no clinically obvious cause for their thrombocytopenia or impaired platelet function 35.5% had raised PSIgG. In order to express the results as number of IgG molecules per platelet, reference curves were created by using FC to measure PSIgG of platelets coated with known amounts of a chimeric IgG (human IgG with murine hypervariable region) monoclonal antibody to the glycoprotein IIb-IIIa complex. Normal platelets had an average 1,463 (SD = 927) molecules of PSIgG. In patients with immune-mediated thrombocytopenia the levels ranged from 690 to 32,328 (mean 11,535) molecules per platelet. Flow-cytometric PSIgG estimation was sensitive, fast and easy to perform and therefore suitable for both research and clinical service purposes.

Adult↗
PubMed1998

Viral safety of blood derivatives by immune neutralization.

Despite careful donor selection and virus inactivation procedures, transmission of viruses by transfusion of blood and blood derivatives is still a threat. Outbreaks of hepatitis A among hemophiliacs having received highly purified, immune globulin depleted coagulation factor concentrates, put the importance of immune neutralization of viruses in blood derivatives in focus. Neutralizing antibodies may block several steps in the virus infection of a cell, from binding of virus to the cellular receptor to the uncoating of virus after uptake in the cell. The efficacy of antibody neutralizing activity depends on the availability and stability of the neutralizing epitopes. Hepatitis A and B viruses are very efficiently neutralized by antibodies and immune escape mutants rarely emerge. Anti-parvovirus B19 antibodies do not fully inactivate the virus, at least in low concentrations, but may prevent development of disease. The neutralizing epitopes on hepatitis C virus and human immunodeficiency virus are located on hypervariable regions of virus membrane proteins. The effects of neutralizing antibodies are thus marginal as immune escape mutants emerge at a relatively high frequency for both viruses. The neutralizing activity of anti-cytomegalovirus antibodies is also questionable as persons may become reinfected with cytomegolvirus despite high levels of antibodies. Plasma and plasma derivatives produced from large donor pools have the potential of being very efficient transmitters of viruses. Neutralizing antibodies are Nature's own, and very important barriers against the spread of many known and unknown viruses contaminating the plasma pools.

Antibodies, Viral↗
PubMed1996

Characterization of the interaction of the monomeric GTP-binding protein Rab3a with geranylgeranyl transferase II.

The monomeric GTP-binding protein Rab3a controls exocytosis in neuroendocrine and neuronal cells. Like other members of the Rab family, Rab3a is posttranslationally modified by the addition of hydrophobic geranylgeranyl groups to its C-terminus. The geranylgeranylation reaction is catalysed by the heterotrimeric geranylgeranyl transferase II. We describe the cDNA cloning of the beta-subunit of human geranylgeranyl transferase II by means of the yeast two-hybrid system. The human enzyme, which is 49% and 96% similar to yeast and rat isoforms, respectively, can complement the beta-subunit deficiency in the yeast strain ANY119. Furthermore, by means of the two-hybrid system and in vitro geranylgeranylation reactions with purified recombinant rat geranylgeranyl transferase II, we have characterized Rab3a domains implicated in the interaction with geranylgeranyl transferase II. We find that the N-terminus, the effector loop, the hypervariable region of the C-terminus, and the geranylgeranyl-acceptor cysteines have roles in this interaction. The GDP-bound form of Rab3a is the preferred substrate of geranylgeranyl transferase II.

Amino Acid Sequence↗