bluuebunny/crossref_metadata_2025 huggingface dataset:
Serologic and molecular analysis of the HLA system in Israeli Jewish patients with oral erosive lichen planus
Authors: Roitberg‐Tambur A. , Friedmann A. , Korn S. , Markitziu A. , Pisanti S. , Satirman C. , Nelken D. , Brauthar C.
Published: December 2008

Abstract: Oral erosive lichen planus is a distinct subtype of the common dermatosis lichen planus. Although the etiology of lichen planus is still obscure, it is known that cell‐mediated immune mechanisms and genetic factors underlie its pathogenesis. Previous studies have found an association between lichen planus and HLA‐DR3 or DR9 in different population groups. The present work was designed to elucidate, at the serologic and molecular levels, whether and which HLA genes are associated with oral erosive lichen planus in Israeli Jewish patients. A significant association with HLA‐DR2 (RR = 4.7; pc < 0.0013) and a decrease in DR4 (RR = 0.3; p < 0.03) among the patients were noted. Oligotyping of DR2 alleles showed the presence of all three common variants (DRB1*1501, DRB1*1502 and DRB1*1601) in the patients, although none of the variants was overrepresented significantly. Three possible explanations for the role of HLA genes in the predisposition to oral erosive lichen planus are discussed. The most attractive theory for the pathogenesis of the disease seems to include the involvement of non‐classical HLA genes.
Analysis of antibody markers, DRB1, DRB5, DQA1 and DQB1 genes and modeling of DR2 molecules in DR2‐positive patients with insulin‐dependent diabetes mellitus
Authors: Sanjeevi C. B. , Lybrand T. P. , Landin‐Olsson M. , Kockum I. , Dahlquist G. , Hagopian W. A. , Palmer J. P. , Lernmark Å.
Published: December 2008

Abstract: HLA‐DR2 is negatively associated with insulin‐dependent diabetes mellitus (IDDM). The aim of the present study was to analyze DR2‐positive patients among 425 consecutively diagnosed unrelated Swedish children with IDDM and in 367 matched controls. HLA‐DRB, ‐DQA and ‐DQB were determined by Taq I restriction fragment length polymorphism analysis. Amplification by polymerase chain reaction (PCR) and hybridization with sequence‐specific oligonucleotide probes was done for DQA1, DQB1 and DRB1 and DRB5. DR2 was positive in 11/425 patients (3%) and 101/367 (28%) controls (OR 0.07, p < 0.0001). Of the 11 DR2‐positive patients, PCR was done in 10, of whom 8 were positive for DRB1*1601‐DRB5*0201 compared to 4/96 (4%) controls (OR 92.0; p<0.001) while the remaining 2 were positive for DRB1*1501‐DRB5*0101 compared to 92/96 (96%, OR 0.01; p<0.001). In 2 patients, a recombination between the haplotypes DQB1*0502‐DQA1*0102 (DQ5)‐DRB1*1601‐DRB5*0201 (DR16 Dw21) and DQB1*0301‐DQA1*0501 (DQ7)‐DRB1*1602‐DRB5*0202 (DR16 Dw22) was observed resulting in the DQB1*0301‐DQA1*0501 (DQ7) DRB1*1601‐DRB5*0201 (DR16 Dw22) haplotypes. The second haplotype was DR3 DQ2 in 6/11 and DR4 DQ8 in 2/11 DR2‐positive patients. In all 3 DQB1*0602‐DQA1*0102‐DR15‐positive patients the second haplotype was DR4‐positive. In order to test whether physicochemical properties of the DR2 molecules were associated with IDDM, we constructed three‐dimentional models of the peptide binding and T‐cell recognition sites (α1 and β1 domains) of five subtypes of DR2‐DRB1, based on the published DR1 crystal structure. No correlations were observed for DR molecule physicochemical properties and diabetes susceptibility. Islet cell antibodies, insulin autoantibodies and GAD65 antibodies, were measured in DR2‐positive patients (n = 11) and controls (n = 101). Despite the presence of the DR2 haplotype the antibody markers were significantly elevated in the patients compared to the controls (GAD65 3/10 patients and 2/101 controls; ICA 7/11 patients and 1/101 controls and IAA 3/11 patients and 0/101 controls). In conclusion, of the five subtypes of DR2, only one, the DRB1*1501, DRB5*0101, DQB1*0602‐DQA1*0102 haplotype, was negatively associated with IDDM. DQ may therefore confer more protection from the disease than DR.
Changes in expression of the cell adhesion molecule PECAM‐1 (CD31) during differentiation of human leukemic cell lines
Authors: Goldberger Amy , Middleton Kelly A. , Newman Peter J.
Published: December 2008

Abstract: PECAM‐1, a member of the immunoglobulin gene superfamily, is widely distributed on cells of the vascular system, and mediates cellular interactions through both homotypic and heterotypic adhesive mechanisms. Previous studies have demonstrated that PECAM‐1 is initially expressed at high levels on CD34+ multipotential progenitors in the bone marrow, but is subsequently downregulated in more committed precursors of all lineages. Interestingly, although PECAM‐1 expression is high on circulating monocytes and neutrophils, little is known about the upregulation of PECAM‐1 expression during terminal myelomonocytic differentiation. We have further characterized this process by examining PECAM‐1 expression during chemically‐induced differentiation of the U937, HL‐60 and HEL cell lines. Quantitative Western blot analysis of cellular lysates indicated that PECAM‐1 expression could be upregulated in U937 and HL‐60 cells by phorbol esters or dimethyl sulfoxide. Northern blot analysis showed that PECAM‐1 mRNA levels appeared to increase in parallel with that of PECAM‐1 protein. We also observed a marked difference in the apparent molecular mass of PECAM‐1 that was lineage‐specific, both in differentiated leukemic cell lines and in their corresponding leukocyte population. Immunofluorescence localization indicated that the cellular distribution of PECAM‐1 in U937 and HL‐60 cells was similar to that of their normal circulating counterparts, and that the pattern of distribution again displayed lineage fidelity. The ability to induce the expression of PECAM‐1 molecules having different glycosylation and surface expression patterns may prove useful for further elucidation of the role of PECAM‐1 in hematopoiesis, as well as studies of the cell lineage‐specific modulation of PECAM‐1 function.
HLA‐B27 subtypes in Asian patients with ankylosing spondylitis Evidence for new associations
Authors: López‐Larrea C. , Sujirachato K. , Mehra N. K. , Chiewsilp P. , Isarangkura D. , Kanga U. , Dominguez O. , Coto E. , Penã M. , Setién F. , Gonzalez‐Roces S.
Published: December 2008

Abstract: The aim of this study was to investigate the contribution of the different B27 subtypes to ankylosing spondylitis (AS) susceptibility. The polymerase chain reaction (PCR) in combination with the sequence‐specific oligonucloetide probes (SSOs) was used to analyse the polymorphism in exon 2 and 3 of HLA‐B27 in two Asian groups with different genetic HLA structures: Indian (I) and Thai (T) populations. The same number of AS patients (45) and healthy B27 positive donors (n=17) from both populations were analysed in order to ascertain the B27 subtypes. Three different findings can be concluded from this study: 1) B*2707 has been found to be associated with AS in both populations. This association has not been previously reported in either ethnic group. 2) B*2704 is strongly associated with AS in the Thai patients (91% in AS vs. 47% in C; RR=11.5; EF=0.83). In contrast, B*2704 was found with similar frequency in Asian Indians AS patients and controls (41% in AS vs. 41% in G). 3) B*2706 was found overrepresented in control populations and absent in AS patients (0% in AS vs. 47% in C; pc<10‐6) showing the maximum value of protective fraction (PF=1). The B*2706 negative association with AS has not been previously described in other ethnic groups and could indicate a protective effect of this subtype on AS susceptibility. The B*2706 allele has two changes relative to B*2704 at residue 114 (His to Asp) and 116 (Asp to Tyr) in the pockets D/E. The importance that these differences can play in the pathogenesis of AS are discussed.
HLA DR and DQ polymorphism in Ashkenazi and non‐Ashkenazi Jews: comparison with other Mediterraneans
Authors: Martinez‐Laso J. , Gazit E. , Gomez‐Casado E. , Morales P. , Martinez‐Quiles N. , Alvarez M. , Martin‐Villa J. M. , Fernandez V. , Arnaiz‐Villena A.
Published: December 2008

Abstract: HLA‐DR and DQ alleles have been detected by DNA typing in Ashkenazi and non‐Ashkenazi Jews from Israel. Allele frequencies, characteristic DR/DQ linkage disequilibria, population distances and their corresponding dendrogram by using the Neighbor‐Joining method were used to study relatedness between Jewish and other Mediterranean and non Mediterranean populations. Closest relatedness is observed between Ashkenazi and non‐Ashkenazi Jews, and, in decreasing order, also with Algerians, Spaniards (including Spanish‐Basques), French and Italians. Also, particular characteristic Central European alleles are observed in Ashkenazi Jews and Mediterranean/African alleles in non‐Ashkenazi Jews. This is consistent with historical data, Jews being an ancient Mediterranean population, who have had a certain degree of admixture with their 2000–3000 years old neighbors in spite of cultural and religious traditions which have preserved identity outside Israel.
HLA‐A, ‐B, ‐C, ‐DR, ‐DQ typing in a population group of Senegal: distribution of HLA antigens and HLA‐DRB1*13 and DRB1*11 subtyping by PCR using sequence‐specific primers (PCR‐SSP)
Authors: Dieye A. , Diaw M. L. , Rogier C. , Trape J.‐F. , Sarthou J. L.
Published: December 2008

One‐hundred‐and sixteen Senegalese Serere were typed for HLA antigens and compared with other ethnic groups in Gambia. We did not find significant differences (Fisher's exact test; P0.01) in the HLA antigens distribution between the Serere and Mandinka groups in Senegal and the Serere, Mandinka and Wolof in The Gambia. The most common HLA haplotypes found (P0.01; Chi square with Yates' correction) were: A1, B8; A2, B51; A32, B44; A33, B58; A2, Cw2; A2, Cw4; A33, Cw3; A2, DR17; A10, DR10; B35, Cw4; B53, Cw6; B57, Cw3; B65, Cw8; B50, DR15; B52, DR4; Cw2, DR17; DR7, DQ2; DR18, DQ4. The HLA‐DRB1*13 and DRB1*11 alleles were subtyped by PCR‐SSP and the frequencies of these alleles in the studied population given. HLA‐DRB1*1304 and DRB1102 were the most common alleles found respectively 15.0 and 18.5%
Three new DPB1 alleles identified in a Bantu‐speaking population from central Cameroon
Authors: Zimmerman P. A. , Steiner L. L. , Titanji V. P. K. , Nde P. N. , Bradley J. E. , Pogonka T. , Begovich A. B.
Published: December 2008

HLA‐DPB1 genotyping of 241 individuals from an African Bantu‐speaking population in central Cameroon using sequence‐specific oligonucleotide probes identified five individuals with novel probe hybridization patterns. DNA sequence analysis of the second exon of the DPB1 alleles from these five individuals identified three new alleles, *6001, *6101N, and *6201. DPB1*6001, found in two individuals, contains a single nucleotide change that results in a polar amino acid, asparagine, at residue 65; this position in the β1 domain is occupied by a nonpolar amino acid in all other reported DPB1 alleles. DPB1*6101N, found in one individual, contains a single base mutation that results in a premature termination codon at position 67. DPB1*6201, found in two individuals, is characterized by the apparent motif shuffling that has been hypothesized to be responsible for the majority of DPB1 sequence polymorphism. These new sequences shed additional light on the potential mechanisms by which allelic diversity is generated at the HLA‐DPB1 locus.
Association between polymorphisms in the TNF region and systemic lupus erythematosus in the Italian population
Authors: D'Alfonso S. , Colombo G. , Bella S. Della , Scorza R. , Momigliano‐Richiardi P.
Published: December 2008

The purpose of this work was to test the hypothesis that MHC encoded susceptibility factors for SLE lie in the TNF region. An association study was performed by analyzing 123 northern Italian SLE patients and 199 matched controls for three TNF markers: two polymorphisms in the TNFA promoter and the TNFa microsatellite. Haplotypic combinations of TNF markers were also compared in patients and controls. No significant association was observed considering either the whole SLE panel or SLE clinical and immunological subtypes. Three TNF‐238/A homozygous patients were detected, while no homozygote was present in controls. The clinical and immunological phenotype of the three ‐238/A homozygotes suggests that the ‐238/AA genotype is a marker of a particular clinical subtype.
A comparison of three statistical models for IDDM associations with HLA
Authors: Graham J. , Kockum I. , Breslow N. , Lernmark Å. , Holmberg E.
Published: December 2008

The association between HLA‐DQ haplotypes and insulin‐dependent diabetes mellitus (IDDM) was studied in 48 children from 44 families ascertained from the high incidence area around Umeå, Sweden. Numerous hypotheses have been proposed to explain associations between HLA and IDDM, but comparisons of statistical models based on these hypotheses have not been attempted. The aim of the present study was to compare the goodness‐of‐fit and predictive abilities among different statistical models. A likelihood‐based analysis rather than a conventional analysis based on contingency tables was therefore adopted. We first used parental haplotype information in a conditional likelihood analysis (1) and then compared this analysis with that of an unaffected control group which used information on geographically matched controls. Under the analysis conditional on parental haplotype, a statistical model motivated by the hypothesis that the entire DQ heterodimer is involved in EDDM pathogenesis fit the data significantly better and had greater predictive ability than either a model motivated by the explanation that an IDDM gene is linked to DQB1 or that the DQB1 chain itself is involved in IDDM pathogenesis, or a model arising from the hypothesis that single amino acids at codon 57 of DQB1 and codon 52 of DQA1, respectively, confer susceptibility. Under the case‐control analysis, the identity of the best‐fitting or most predictive statistical model was not as clear, although both approaches to analyzing risk suggested that the single‐amino‐acids model had significantly poorer fit compared to the remaining two models.
Lymphocytes subsets in normal individuals: analysis by four color immunofluorescence and flow cytometry on whole blood
Authors: Schiavon V. , Roth P. , Bolton W. E. , Farcet J. P. , Bensussan A. , Boumsell L.
Published: December 2008

In order to precisely define human lymphocytes subsets, we used four color immunofluorescence analysis and flow cytometry. We report here the results of systematic studies performed on whole blood from 20 normal volunteers. This was performed using monoclonal antibodies recognizing 18 different CD molecules and analyzed here into 14 different 4‐color immunofluorescence combinations. This showed that among T cells, the two major CD3+CD8+ and CD3+CD8‐ subsets differed greatly in the percentage of cells expressing CD26, CD27, CD28, CD38, CD45RA, CD45RO, CD57, S6F1, BY55, CD101 and their respective combination representing an array of subsets. Furthermore the minor NK subsets, i.e. CD2+CD3‐CD8+, CD2‐CD3‐CD8+, CD2+CD3‐CD8‐, CD2‐CD3‐CD8‐ also differed in percentages of cells expressing CD16, CD56, CD57, S6F1, BY55 and their combinations.
A novel recombinant HLA‐B*39 allele (B*3910) in a South African Zulu
Authors: Wells R. S. , Parham P.
Published: December 2008

The sequence of a new B*39 allele has been identified in a South African Zulu individual. This allele, designated B*3910, differs at two nucleotide positions (246 and 272) from B*39011. The difference at position 246 is silent, while that at position 272 results in an amino acid change from cysteine (B*39011) to tyrosine (B*3910). As these same differences are found in other HLA‐B alleles, they were probably introduced into the B*3910 sequence by a short gene conversion event with another allele. This finding provides further evidence for the diversification of HLA‐B allelic sequences via recombination.
Nomenclature for factors of the HLA system, update July 1996
Authors: Marsh Steven G. E.
Published: December 2008

The following sequences have been submitted to the Nomenclature Committee since the June 1996 Nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in the forthcoming report Nomenclature for factors of the HLA System, 1996 Below are listed the newly assigned sequences, confirmations of previously reported sequences and some sequences which are corrections of those originally reported. The accession number of each sequence is given and these can be used to retrieve the sequence files from either the EMBL, GenBank or DDBJ data libraries. Although accession numbers have been assigned by the data libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released, in such a case you will have to contact the submitting author directly.
Stimulation through CD50 (ICAM‐3) induces both activation and programmed cell death of human thymocytes
Authors: Martínez‐Cáceres E. , Ruggiero G. , Spits H. , Juan M. , Barcelo J. , Vives J. , Martorell J. , Vinas O.
Published: December 2008

CD50 (ICAM‐3) has been identified as the third CD 11a/CD 18 (LFA‐1) counter receptor. We investigated the expression and possible role of this molecule in the induction of early and late activation events in human thymocytes. We observed that CD50 expression is acquired by early T cell progenitors (CD34+) and maintained during thymic development, reaching the highest levels in the most mature population of thymocytes (CD3high). Neither basal nor cytokine‐induced expression of CD50 was observed on untransformed human thymic epithelial cell lines. Cross‐linking of CD50 expressed on the surface of human thymocytes, by using mAbs recognizing epitopes not related to the CD1 la binding site, transduced transmembrane signals leading to an increase of intracellular calcium concentration. This calcium mobilization was inhibited when CD50 was co‐cross‐linked with CD45, suggesting that tyrosine phosphorylation is also involved in CD50 signaling. The same anti‐CD50 mAbs that were able to affect intracellular calcium levels were shown to induce CD69 but not CD25 expression on human thymocytes. This effect was preferentially observed on CD3low/CD3high thymocyte subpopula‐tions. Cross‐linking of CD50 also significantly increased activation‐induced cell death of human thymocytes. These results support the idea that CD50 molecule can play a role in developing functionally mature T lymphocytes.
MHC class II alleles and haplotypes in patients with pemphigus vulgaris from India
Authors: Delgado J. C. , Yunis D. E. , Bozón M. V. , Salazar M. , Deulofeut R. , Turbay D. , Mehra N. K. , Pasricha J. S. , Raval R. S. , Patel H. , Shah B. K. , Bhol K. , Alper C. A. , Ahmed A. R. , Yunis E. J.
Published: December 2008

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‐DRB 1 * 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‐DQB 1*0302 (p=0.03). An identical amino acid sequence (Leu‐Leu‐Glu‐Arg‐Arg‐Arg‐Ala‐Glu), in positions 67–74 of the P 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 DQB 1*0503 and the association with HLA‐DR14 alleles would be the result of linkage disequilibrium. Third, the HLA‐DRB 1 locus susceptibility could involve a specific amino acid sequence in the third hypervariable region shared by several HLA‐DR14 alleles.
Development of PCR‐SSOP for HLA‐A typing of bone marrow registry donors
Authors: Williams F. , Mellon E. , Middleton D.
Published: December 2008

A medium resolution PCR‐SSOP typing method, using 26 digoxigenin labelled probes, has been established for the identification of HLA‐A alleles. The system is capable of discriminating all of the serologically defined specificities except for eight heterozygous combinations which are however rare in Caucasians. The method has been applied to 1,838 individuals on the local bone marrow registry who either had only one detectable HLA‐A antigen, or a HLA‐A antigen whose presence had been queried using the serological technique or a broad HLA‐A specificity assigned by the serological technique. In all but one case the serologically assigned antigens were detected with the PCR‐SSOP method. In addition, PCR‐SSOP detected the presence of a second HLA‐A allele in over 10% of individuals who had been previously homozygous. Frequency information, based on a population of 5,000 individuals, has been established using a combination of molecular and serological typing data.
MHC‐DRB allelic sequences incorporate distinct intragenic trans‐specific segments
Authors: Gaur L. K. , Nepom G. T. , Snyder K. E. , Anderson J. , Pandarpurkar M. , Yadock W. , Heise E. R.
Published: December 2008

The second exon of primate MHC‐DRB genes encodes discrete areas of allelic hypervariability (HVR), which are used as the basis for lineage assignments to determine genetic and evolutionary relationships. Comparisons of these regions have led to the “trans‐species hypothesis”, which proposes that certain MHC alleles from one species are more closely related to those from other species than they are to each other; i.e., that allelic lineages are ancestral in origin. We evaluated this paradigm in an analysis of macaque and baboon MHC‐DRB genes using oligotyping and sequencing of 87 new nonhuman primate DRB alleles. A remarkable conservation of sequence motifs in the HVRIII region (codon 60–79) was observed, detected both by hybridization and by sequencing; some of these motifs were found in species such as prosimians that have diverged from the human lineage 50 MYA. However, these fixed HVRIII motif sequences nevertheless occur on a background of diverse lineages suggesting that it is the segmental motif, rather than the allele per se which is trans‐specific in origin. Sequences within the first hypervariable region (codons 7–14) identified lineage assignments to several DRB loci (DRB1, DRB3, DRB4, DRB5, DRB6 and DRB7), although a large number of DRB nucleotide sequences did not correspond to a defined allelic motif, suggesting that many of the nonhuman sequences lack human HVRI homologs and have accumulated additional intraspecies variation subsequent to speciation. While there are certain allelic lineages in HVRI that show trans‐species conservation, other sequence motifs seem purely species‐specific. These differences suggest that HVRI and HVRIII regions have distinct mechanisms for maintenance of trans‐specific sequence elements, with different evolutionary histories for segmental nucleotide conservation.
HLA‐B typing by allele separation followed by direct sequencing
Authors: Eberle M. , Knapp L. A. , Iwanaga K. K. , Domanico M. J. , Aiyer K. , Watkins D. I.
Published: December 2008

Due to the enormous allelic diversity of the HLA‐B locus, it has been difficult to design an unambiguous molecular typing method for the alleles at this locus. Here we describe a technique for the direct sequencing of HLA‐B alleles. Initially, HLA‐B alleles were PCR‐amplified after locus‐specific reverse transcription of RNA. Alleles were then separated using denaturing gradient get electrophoresis (DGGE), which separates DNA fragments based on their sequence composition. Amplification products were excised from the gel and eluted DNA was reamplifled and directly sequenced. The derived sequences were aligned to a database of published HLA‐B sequences, and an initial allele assignment was made. This approach was theoretically sufficient to type 92 of the 118 known HLA‐B alleles. The majority of the remaining 26 alleles contain differences at the beginning of exon 2, a region outside the DGGE‐separated PCR products. Therefore, we used heterozygous sequencing of this region to identify 19 of these 26 alleles, raising the resolution power to 111 alleles. Using this technique, we analyzed immortalized cell lines and blood samples from several different sources. Nine immortalized cell lines were obtained from the 10th International Histocompatibility Workshop (IHWS) and nine were derived from aboriginal peoples. Additionally, 25 blood samples were acquired from a panel of donors previously shown to be difficult to type using serological techniques. Altogether, using this new method of allele separation by DGGE followed by direct sequencing, we typed 52 different alleles from 57 individuals, covering 40 serological specificities.
Dominant clones in immortalized T‐cell lines from rheumatoid arthritis synovial membranes
Authors: Saadawi A. M. , L'Faqihi F. , Diab B. Y. , Sol M. A. , Enault G. , Coppin H. , Cantagrel A. , Biesinger B. , Fleckenstein B. , Thomsen M.
Published: December 2008

Transformation of human T cells by herpesvirus saimiri allows the production of an unlimited number of T cells which express a functional T‐cell receptor. In this study we transformed four T‐cell lines derived from rheumatoid arthritis synovial membranes. The transformed T cells were mainly CD4+ and expressed the phenotype of activated T cells. They were grown for more than 1 year in the absence of mitogen or feeder cells, and three of them could be maintained without exogenous LL‐2. The presence of viral DNA in the transformed cells was shown by in situ hybridization with a probe from the H‐DNA region of the virus. No infectious virus could be recovered from the transformed cells. The relative proportion of the 24 different Vβ families between the four transformed lines showed variations that increased with time. In the two T‐cell lines transformed at an early stage of culture, the Vβ2 family was maintained at about 10%. The dominant Vβ2 clones that previously have been characterized in the patient were found in all transformed T‐cell lines. We have thus shown the feasibility of obtaining transformed T cells from synovia] membranes. They contain the dominant clones that are considered of potential importance for the disease, permitting further functional studies.
HLA‐B*5603: sequence of a novel hybrid allele comprising B*56 and B*4601 segments
Authors: Barnardo M. C. N. M. , Bunce M. , Lord C. J. , Welsh K. I.
Published: December 2008

The sequence of B*5603 has been deposited with the Genome Sequence Database and has the accession number U73113. The name B*5603 has been officially assigned by the World Health Organization (WHO) Nomenclature Committee in September 1996. This follows the agreed policy that, subject to the conditions stated in the most recent nomenclature report (1), names will be assigned to new sequences as they are identified. Lists of such new names will be published in the following WHO nomenclature report. CJL is a Wellcome Trust prize student.
Genomic organization of a human killer cell inhibitory receptor gene
Authors: Wilson M. J. , Torkar M. , Trowsdale J.
Published: December 2008

We have cloned a region of human chromosome 19q13.4 which contains multiple killer cell inhibitory receptor (KIR) loci. By random and directed sequence analysis of these KIR‐specific clones, we deduced the genomic structure of KIR genes. A locus encoding a member of the NKAT‐2 family of KIRs is presented here. The structure of the gene is reminiscent of loci of the Fc receptor gene family, and the two sets of genes may derive from a common ancestor. The KIR gene contains potentially nine exons. The first two exons encode the leader sequence, as in Fc receptor genes. The third exon encodes an untranslated pseudo exon specifying an immunoglobulin domain with an in‐frame stop codon. Expressed cDNAs do not contain this exon. This finding is consistent with the hypothesis that certain KIR genes may have been derived from the duplication of a primordial three immunoglobulin domain structure with subsequent skipping of one exon to derive genes with two expressed immunoglobulin domains. Variation in numbers of immunoglobulin domains in different KIR genes is facilitated by conservation of splicing frame in respect to the codon triplet for each immunoglobulin domain.
Possible association between HLA antigens and the response to interferon in Japanese patients with chronic hepatitis C
Authors: Miyaguchi S. , Saito H. , Ebinuma H. , Morizane T. , Ishii H.
Published: December 2008

Correlation between the major histocompatibility complex class I antigens (HLA‐A, ‐B and ‐C) and the elimination from serum of hepatitis C virus in patients with chronic hepatitis C has not been understood. We analyzed HLA phenotypes and their relationship to the efficacy of interferon treatment. Of the 172 patients who were treated with 9 million units of interferon‐α2a three times a week for 6 months, 54 patients were responders and 118 patients were non‐responders. No significant difference was observed between the 172 patients and 199 healthy subjects with regard to the frequencies of HLA‐A, ‐B and ‐C antigen phenotypes. However, HLA‐B55, B62, CW3 and CW4 frequencies were significantly higher in responders than in non‐responders to the interferon treatment. CW4 was found to link with B62, but other phenotypes were independent each other. Patients with HLA B55, B62 and CW3 had a significantly lower viral load, and showed a better response to interferon. These results suggest that HLA system does not have an influence on the evolution towards chronicity of the disease due to hepatitis C virus, but HLA B55, B62 or CW4, and CW3 may be a virus quantity‐regulating factors which then affect to response to the interferon treatment, indicating that these HLA antigens in conjunction with a viral peptide is a key target antigen for cytotoxic T lymphocytes in patients with chronic hepatitis C.
Analysis of critical residues of HLA‐DQ6 molecules in insulin‐dependent diabetes mellitus
Authors: Sanjeevi C. B. , DeWeese C. , Landin‐Olsson M. , Kockum I. , Dahlquist G. , Lernmark A. , Lyhrand T. P.
Published: December 2008

Among DQ6 molecules, DQA1*0102‐DQB1*0602 is negatively associated with insulin‐dependent diabetes mellitus (IDDM), but DQA1*0102‐DQB1*0604 shows a neutral to positive association in Swedish children with IDDM. The aim of this study was to identify critical DQB1 residues that may account for the differences in IDDM association observed for these two DQ6 molecules. HLA‐DQ genotyping in 425 IDDM patients and 367 matched controls showed DQ6 (B1*0602) in 1% of patients and 25% of controls (odds ratio (OR) 0.02). DQ6 (B1*0604) alone was neutral (9% of patients and 10% of controls) but in combination with DQ8, was positively associated (5% of patients, 1% of controls, OR 9.49). In both these DQ6 molecules the ã‐chain is the same but the β‐chain differs at positions 9, 30, 57, 70, 86 and 87. DQB1*0602 has F9, Y30, D57, G70, A86 and F87, whereas DQB1*0604 has Y9, H30, V57, R70, G86 and Y87. Three‐dimensional models of the two DQ6 molecules, based on crystal coordinates of the homologous DR1 molecule, suggest that residue 57β will likely play a critical role in peptide‐binding selectivity, whereas residue 70β is probably a major contact site for the T‐cell receptor. The effects of these specific polymorphic substitutions in DQ molecules on peptide binding and T‐cell receptor recognition may be sigmficant in IDDM susceptibihty.
Triplet repeat polymorphism in the NOTCH4 gene within the human major histocompatibility complex in a healthy population and patients with a salivary gland tumor in Japan
Authors: Ando A. , Sugaya K. , Shigenari A. , Naruse T. K. , Horiuchi M. , Shiina T. , Kawata H. , Chen L. , Ikemura T. , Inoko H.
Published: December 2008

The NOTCH4 gene, the human counterpart of the mouse mammary tumor gene, int‐3, has been recently localized near the boundary of the HLA class II and class III regions. This gene is one of candidates for development of salivary gland tumor. Microsatellite polymorphism of (CTG)n repeat in the signal peptide domain of NOTCH4 was analyzed in Japanese including the patients with salivary gland tumor. Four alleles consisting of 6, 9, 10 and 11 repetitions of CTG (Leu) were observed and found to be in linkage disequilibria with HLA class I and class II alleles. No significant association if this microsatellite polymorphism with the disease were observed in 26 samples of salivary gland tumor. In this neoplasia, neither large‐scale deletion nor translocation was detected around the NOTCH4 gene using genomic Southern hybridization analysis by the NOTCH4 cDNA as aprobe.
The search for HLA‐matched donors: a summary of HLA‐A*, ‐B*, ‐DRB1/3/4/5* alleles and their association with serologically defined HLA‐A, ‐B, ‐DR antigens
Authors: Hurley C. K. , Schreuder G. M. T. , Marsh S. G. E. , Lau M. , Middleton D. , Noreen H.
Published: December 2008

This report summarizes data obtained from several large studies including the WHO HLA Nomenclature Committee, the International Cell Exchange, UCLA, the British Society for Histocompatibility and Immunogenetics Rare Cell Exchange and the National Marrow Donor Program and individual laboratories aimed at identifying a serologic type for specific HLA‐A,‐B,‐DRB allelic products. Alleles that are poorly characterized at the serologic level are indicated and an approach is suggested for obtaining the information needed to clarify their serologic typing. The tables provided will be useful in guiding searches for an unrelated donor in which patient and/or potential donors are typed either by serology or by DNA‐based methods and will provide a “dictionary” of potential equivalents between HLA “types” obtained by the two methods.
Significance of tumor necrosis factor microsatellite polymorphism in renal transplantation
Authors: Asano H. , Kobayashi T. , Uchida K. , Hayashi S. , Yokoyama I. , Inoko H. , Takagi H.
Published: December 2008

Plasma levels of tumor necrosis factor (TNF) α are raised during acute rejection following organ transplantation. Variations in TNF á production have been found to be associated with the polymorphism of TNF microsatellite. Therefore, there is a possibility that a transplant recipient with some type of TNF microsatellite can be a high‐risk patient of graft rejection. The purpose of this study was to examine whether TNF microsatellite polymorphism is related to acute allograft rejection. We investigated the relation of two microsatellites, TNFa and TNFd, to acute rejection after renal transplantation. Among 189 primary living‐related renal transplantations from one haplotype‐mismatched and one DRBI‐mismatched donor, we analyzed TNF microsatellites of 163 patients whose DNA were available to this study. The frequency of the TNFa9 microsatellite allele was significantly higher in the rejection group compared to the rejection‐free group. In contrast, the frequency of TNFd4 was significantly lower in the rejection group compared to the rejection‐free group. TNFa9 and TNFd4 showed strong associations with HLA‐B35 and B44, respectively. However, the TNF microsatellite locus was more closely related to acute rejection than HLA‐B. It was suggested that the analysis of TNF microsatellite polymorphism can provide useful information in predicting prognosis after transplantation.
Identification of a new DRB3*02 allele (DRB3*0207) by sequence‐based typing
Authors: Voorter C. E. M. , Hentges F. , van den Berg‐Loonen E. M.
Published: December 2008

A new DRB3*02 allele (DRB3*0207) was detected in a female Luxembourg Caucasian blood donor by sequence‐based typing. The new allele differs from DRB3*0202 by two substitutions in codon 57 resulting in an amino acid change from a charged aspartic acid to a neutral valine. This is the first example of a DRB3 allele pair differing only at codon 57.
Fluorotyping of HLA‐C: differential detection of amplicons by sequence‐specific priming and fluorogenic probing
Authors: Luedeck H. , Blasczyk R.
Published: December 2008

Conventional PCR‐SSP, which is based on an agarose gel‐based read‐out, has the disadvantages of time‐consuming post‐PCR steps and low potential for automation. The aim of our study was to sort out these drawbacks by establishing a fluorescence‐based PCR‐SSP system for HLA‐C. The assay relies on the sequence‐specific identification of amplicons with individually labeled probes that are cleaved during successful PCR by the 5′‐3′ exonuclease activity of the Taq‐DNA Polymerase. The oligonucleotides are labeled with a unique and spectrally resolvable fluorescent reporter dye at the 5′ terminus (FAM or TET) and a common quencher dye at the 3′ terminus (TAMRA). In case of amplification, the reporter escapes from the quenching control caused by the physical separation of the dyes, resulting in a significant increase of the reporter fluorescence. This allows simultaneous and differential detection of the specific HLA (FAM) and internal control (TET) product. The HLA‐C fluorotyping information is based on the individual reporter fluorescence released by 18 PCR primer mixes. Using this method, we analyzed 145 samples previously typed with conventional PCR‐SSP and found a concordance rate of 100%. Furthermore, fluorotyping revealed quantitative results that may indicate the presence of homozygosity by high signal intensities. This provided extra protection not to miss new alleles which are not amplified by the current primer mixes. These features as well as the capability of high sample throughput and the possibility of automation makes fluorotyping an attractive tool for PCR‐based HLA typing.
HLA class II associations in juvenile Graves' disease: indication of a strong protective role of the DRBl*0701, DQAl*0201 haplotype
Authors: Lavard L. , Madsen H. O. , Perrlld H. , Jacobsen B. B. , Svejgaard A.
Published: December 2008

Previous studies have shown that HLA‐DRB1*0301 and DQA1*0501 are associated with susceptibility to Graves' disease. Ninety Danish patients with early onset of Graves' disease and 102–192 controls were analyzed for HLA‐DR and ‐DQ to investigate if the same associations exist in the juvenile form of Graves' disease. Both DRB1*0301 and DQA1*0501 were highly significantly increased in the patients with relative risks of 8.0 and 4.6, which are higher than those seen in adults. Stratification showed that DRB1*0301 is more strongly associated than DQA1*0501. Surprisingly, the DRB1*0701, DQA1*0201 haplotype was completely absent from this group of patients, indicating a strong protective role of this haplotype in juvenile Graves' disease.
Mhc‐E polymorphism in Pongidae primates: the same allele is found in two different species
Authors: Suárez B. , Morales P. , Castro M.J. , Fernández‐Soria V. , Recio M.J. , Pérez‐Bias M. , Alvarez M. , Díaz‐Campos N. , Arnaiz‐Villena A.
Published: December 2008

Mhc‐E intron 1, exon 2, intron 2, and exon 3 from pygmy chimpanzee (Pan paniscus), chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) have been sequenced; six new Mhc‐E alleles have been obtained but sequence changes are only placed either in introns or in synonymous exonic bases. One pygmy chimpanzee Mhc‐E DNA sequence is identical to another sequence from chimpanzee; the fact that no variation is found also at the intronic level suggests that these two species of chimpanzee may have recently separated and/or that both of them might only represent subspecies. Mhc‐E phylogenetic trees separate two evolutionary groups: Pongidae, including humans, and Cercopithecinae; this is also found by studying another non‐classical class I gene, Mhc‐G. The Mhc‐E alleles' invariance at the protein level supports that strong selective forces are operating at the Mhc‐E locus, as has also been found in both Cercopithecinae and humans. These allelic and evolutionary data suggest an altogether different functionality for HLA‐E (and also HLA‐G) compared with classical class I proteins: i.e., sending negative (tolerogenic) signals to NK and T cells.
High frequency of altered HLA class I phenotypes in invasive colorectal carcinomas
Authors: Cabrera T. , Collado A. , Fernandez M.A. , Ferron A. , Sancho J. , Ruiz‐Cabello F. , Garrido F.
Published: December 2008

Abstract: We analyzed the expression of HLA class I antigens in 78 tumor tissue samples obtained from patients diagnosed as having colorectal carcinomas. A broad panel of mAbs defining HLA monomorphic, locus‐specific and allele‐specific determinants was used. In addition, an antibody defining HLA‐C locus‐specific determinant (L31) was also tested. Previous reports on these tumors indicated HLA class I losses of 30 to 40%. At least 73% of the patients in the present study had a detectable HLA class I alteration. These altered HLA phenotypes were classified as total HLA loss (18%) (phenotype I); HLA‐A locus‐specific loss (9%) (phenotype ma); HLA‐B locus‐specific loss (8%) (phenotype IIIb); HLA‐A and B locus losses (2%) and HLA allelic losses (36%) (phenotype IV). We found no HLA‐C locus losses. Autologous peripheral blood lymphocyte HLA class I typing was always necessary to define phenotype IV. We also studied the CD3 zeta chain in tumor tissues to correlate possible changes in the CD3 signal transduction pathway with HLA alterations. The CD3 ratio was frequently altered, but this alteration could not be correlated with tumor HLA phenotypes. The high frequency of HLA class I losses in colorectal carcinomas suggests that this finding is a widespread phenomenon and may be required to escape T‐cell recognition. It remains to be determined whether HLA expression is “normal” in the rest of the 27% of our patients.
Purification and characterization of a human sialoglycoprotein antigen expressed in immature thymocytes and fetal tissues
Authors: Cecco L. , Bond H.M. , Bonelli P. , Tuccillo F. , Cerra M. , Tassone P. , Sorice R. , Lamberti A. , Morrone G. , Venuta S.
Published: December 2008

Abstract: The monoclonal antibody UN1 was previously produced in our laboratory on the basis of selective reactivity with human thymocytes and has been classified as unclustered by the 5th and 6th International Workshop and Conference on Human Leukocyte Differentiation Antigens. The antigen recognized by mAb UN1 was found to be expressed on the cell surface of immature human thymocytes, a subpopulation of peripheral T lymphocytes and on several fetal tissues including thymus. The UN1 antigen is purified from children's thymus by ion‐exchange and affinity chrom‐atography. Two‐dimensional electrophoresis shows that the purified antigen displays microheterogeneity appearing as multiple spots over a pI range 4.4–5.0 at 100–120 kDa. Treatment with neuraminidase results in a retarded migration in SDS‐PAGE, an increase in isoelectric point and a reduction in carbohydrate content, indicating a substantial content of sialic acid. Glyco‐sidase digestion and lectin‐binding analysis indicate that the carbohydrate residues are essentially O‐linked. A preliminary analysis has detected the UN1 antigen in human breast carcinoma tissues but not in normal breast. The biochemical features and the pattern of expression of the UN1 antigen indicate that this molecule may have the characteristics typical of the family of cell‐membrane‐associated mucin‐like glycoproteins; a number of these molecules are thought to have a role in cell‐cell interaction, tumor progression and metastasis.
HLA‐A towards a high‐resolution DNA typing
Authors: Scheltinga S.A. , Williams F. , van der Zwan A.‐W. , Rozemulier E.H. , Middleton D. , Tilanus M.G.J.
Published: December 2008

Abstract: Sequencing‐based typing (SBT) and sequence‐specific oligonucleotide probing (PCR‐SSOP) are DNA‐based typing approaches to identify HLA‐A alleles. In this study PCR‐SSOP SBT have been evaluated and considered to reach a high‐resolution typing. Based upon serological typing, 32 genomic samples were typed by SBT and PCR‐SSOP. Three main clusters of resolution could be defined. The advantage of the PCR‐SSOP approach is the possibility to type numerous samples in a short time. SBT minimizes the number of ambiguous heterozygous combinations and often allows direct detection and identification of new alleles.
Improvement of HLA class I and class II PCR‐SSP typing by using timed‐release activity of DNA polymerase
Authors: Chen D.‐F. , Seibert I. , Chen H.‐Y. , Herbst‐Kiene I. , Pastucha L.T. , Stangel W.
Published: December 2008

Abstract: Variable amounts of non‐specific amplification may occur in HLA PCR‐SSP typing, and this can be significantly reduced by the use of AmpliTaq Gold. In an effort to achieve an optimal balance between specificity and efficiency of the PCR amplification for both HLA alleles and the internal control, we designed a system of timed‐release activity by combining two different Taq DNA polymerases. The reaction was started at a relatively low level of enzyme activity and as thermal cycling progressed more and more Ampli‐Taq Gold was slowly activated for the reaction to continue. We applied this system to all routine HLA PCR‐SSP typing. The number of repeat typings due to non‐specific amplification and/or amplification failure of the internal control was remarkably reduced.
Increased level of serum HLA class I antigens in patients with systemic lupus erythematosus. Correlation with disease activity
Authors: Brescianl A. , Pirozzi G. , Spera M. , Lombardi M.L. , Ambrosone L. , Migliaresi S. , Ferrone S. , Manzo C.
Published: December 2008

Abstract: The level of soluble pYn‐assoriated HLA Class I heavy chains (sHLA‐I) and of soluble β2‐μ‐free HLA Class I heavy chains (sHLA‐FHC) was found to be significantly higher in sera from 58 patients with systemic lupus erythematosus (SLE) than in those from 82 age and sex‐matched controls. The level of serum sHLA‐I in patients with SLE was significantly correlated to disease activity. Western blotting analysis showed that the 44‐kDa isoform represents the major component in the antigens immuno‐precipitated by anti‐β2‐μ mAb NAMB‐1 and by anti‐β2‐μ‐free HLA Class I heavy chain mAb HC‐10 from sera of patients with SLE. These results suggest that the increased serum levels of sHLA‐I and of sHLA‐FHC in patients with SLE reflect their increased shedding from cell membrane. In view of the ability of sHLA‐I and of sHLA‐FHC to induce apoptosis of activated T cells, it is suggested that their increased serum levels in patients with SLE is triggered by dysregulation of the immune system leading to T‐cell activation. The increased serum levels of sHLA‐I and of sHLA‐FHC may be used by the immune system to control the pool of activated T cells by inducing apoptosis. If this possibility is proven to be correct, modulation of the serum level of sHLA‐I and of sHLA‐FHC may be utilized to develop strategies to treat SLE.
Distribution of HLA class II alleles among Spanish patients with pemphigus vulgaris
Authors: González‐Escribano M.F. , Jiménez G. , Walter K. , Montes M. , Perez‐Bernal A.M. , Rodríguez M.R. , Conejo‐Mir J.S. , Núñez‐Roldán A.
Published: December 2008

Abstract: Twenty‐six unrelated Spanish Caucasian individuals affected by pemphigus vulgaris (PV) were HLA typed and frequencies compared with those of 200 ethnically matched healthy controls. Twenty‐three out of 26 patients were HLA‐DR4. The frequency of HLA‐DR14 was also increased (31%; controls: 4%). Of the 23 patients positive for HLA‐DR4, 21 carried the DRB1*0402 allele. Therefore, the frequency of HLA‐DRB1*0402 among patients was 81% (4% in controls; P=4.7times 10‐27, OR=100.8). Interestingly, HLA‐DR13, a frequent HLA‐DR specificity in the Spanish general population (27%), was absent among the PV patients (P=0.009; Pc=0.1; OR=0.05). Taking together these data, we can conclude that, in the Spanish population, PV is preferentially and strongly associated with HLA‐DRB1*0402, whereas DRB1*13 seems to confer a protective effect in our population.