bluuebunny/crossref_metadata_2025 huggingface dataset:
HLA class II alleles in Japanese patients with inflammatory bowel disease
Authors: Yoshitake S. , Kimura A. , Okada M. , Yao T. , Sasazuki T.
Published: March 2003

The association of various HLA class II loci with Crohn’s disease (CD) and ulcerative colitis (UC) has yet to be fully elucidated. To determine whether there is an association of HLA class II genes (DR, DQ and DP alleles) with inflammatory bowel disease (IBD), HLA class II genes for polymorphisms were analyzed at the DNA level in 111 patients with CD, 81 with UC and 525 healthy controls by the polymerase chain reaction‐sequence specific oligonucleotide probe method. Allele and haplotype frequencies were compared between these populations. Results were as follows: 1) the presence of DQB1*0402 (RR=3.90, Pc=0.0001) was positively associated with CD; 2) the presence of DRB1*1502 (RR=4.51, Pc<1×10−8), DRB5*0102 (RR=4.70, Pc<1×10−8), DQA1*0103 (RR=3.72, Pc=1×10−5), DQB1*06011 (RR=3.78, Pc=1×10−5), DPA1*0201 (RR=3.23, Pc=0.0001) and DPB1*0901 (RR=4.83, Pc<1×10−8) was positively associated and that of DRB4*0101 (RR=0.20, Pc<1×10−8) and DQA1*0302 (RR=0.34, Pc=0.001) negatively associated with UC; 3) haplotype analysis showed a positive association between the presence of DRB1*0410‐DQA1*0302‐DQB1*0402 and DRB1*0802‐DQA1*0401‐DQB1*0402 with CD, and a negative association between the presence of DRB1*1502‐DQA1*0103‐DQB1*06011 and CD, there was no association of DRB1*08032‐DQA1*0103‐DQB1*06011 with CD; and 4) in UC, a positive association with the presence of DRB1*1502‐DQA1*0103‐DQB1*06011 was found, but DRB1*08032‐DQA1*0103‐DQB1*06011 was not associated with it. In conclusion, in CD in the Japanese population, HLA‐linked disease susceptibility alleles appear to be DQB1*0402 and DRB1*1502, a disease resistance allele. In UC, DRB1*1502 appears to be a disease susceptibility allele.
Contribution of TAP genes to genetic predisposition for diffuse panbronchiolitis
Authors: Keicho N. , Tokunaga K. , Nakata K. , Taguchi Y. , Azuma A. , Tanabe K. , Matsushita M. , Emi M. , Ohishi N. , Kudoh S.
Published: March 2003

Diffuse panbronchiolitis is a chronic obstructive pulmonary disease found in Asian populations. Although diffuse panbronchiolitis is considered to be a multifactorial disease of unknown etiology, the disease susceptibility appears to be determined by a genetic predisposition unique to Asians. An earlier study showed that human leukocyte antigen (HLA)‐B54 predominantly found in East Asians was strongly associated with the disease. A possible interpretation of this association is that the class I molecule or class I antigen presenting system is directly involved in its pathogenesis. Recent observations in which impaired expression of class I molecules causes a syndrome resembling diffuse panbronchiolitis further prompted us to test this possibility. Genes of the molecules implicated in the class I pathway, TAP1, TAP2 and LMP2, which are located in the HLA region of the sixth chromosome were analyzed in 76 patients with diffuse panbronchiolitis and 120 normal controls. The combination of Ala‐665 and Gln‐687 in exon 11 of the TAP2 gene was associated with the disease (P=0.0028, Pc<0.05). Although this positive association might be partly explained by linkage disequilibrium with HLA‐B*5401, this TAP2 variation was associated with the disease even in the B*5401‐negative subgroup. On the other hand, the His‐60 substitution within the LMP2 gene exhibited a negative association with the disease. This negative association, however, could be explained by a strong linkage disequilibrium with HLA‐B44 which showed a negative association with the disease in the previous study. These results support the notion that diffuse panbronchiolitis is influenced by genetic factors in the HLA region. Besides the class I gene itself, genes relevant to the class I antigen presenting system might contribute to its genetic predisposition.
HLA class II haplotypes in primary sclerosing cholangitis patients from five European populations
Authors: Spurkland A. , Saarinen S. , Boberg K.M. , Mitchell S. , Broome U. , Caballeria L. , Ciusani E. , Chapman R. , Ercilla G. , Fausa O. , Knutsen I. , Pares A. , Rosina F. , Olerup O. , Thorsby E. , Schrumpf E.
Published: March 2003

The association of primary sclerosing cholangitis (PSC) to HLA class II genes was studied by comparing patients from five different European populations. Deduced HLA‐DRB1, DQA1, DQB1 haplotypes of 256 PSC patients from England, Italy, Norway, Spain and Sweden were compared to those observed in 764 ethnically‐matched controls. Increased frequencies of the DRB1*03, DQA1*0501, DQB1*02 (RR=3.0, P<0.00001) and the DRB1*13, DQA1*0103, DQB1*0603 haplotypes (RR=2.4, P<0.0001) were observed in all five patient groups. A total of 16% of the PSC patients were homozygous for the DRB1*03, DQA1*0501, DQB1*02 haplotype compared to 1% of the controls (RR=20, P<0.0001). The DRB1*04, DQA1*03, DQB1*0302 haplotype was significantly reduced in frequency(RR=0.4, P<0.00001). Among Norwegian, Swedish and British patients that did not carry neither the DRB1*03, DQA1*0501, DQB1*02 nor the DRB1*13, DQA1*0103, DQB1*0603 haplotype, an increased frequency of the DRB1*15, DQA1*0102, DQB1*0602 haplotype was observed (RR=2.0, P<0.0001). Thus, PSC was found to be positively associated to three different HLA class II haplotypes (i.e. the DRB1*03, DQA1*0501, DQB1*02, the DRB1*15, DQA1*0102, DQB1*0602 and the DRB1*13, DQA1*0103, DQB1*0603 haplotypes) and negatively associated to one HLA class II haplotype (i.e. the DRB1*04, DQB1*0302 haplotype).
Single strand conformational polymorphism analysis of human CD1 genes in different ethnic groups
Authors: Oteo M. , Parra J.F. , Mirones I. , Giménez L.I. , Setién F. , Martínez‐Naves E.
Published: March 2003

CD1 molecules are able to present unusual antigens, lipids or glycolipids from mycobacterium cell walls to T lymphocytes. Previous studies have suggested that polymorphism of these genes is very limited, in contrast with classical major histocompatibility complex (MHC) antigen‐presenting molecules. Our aim was to study possible allelic variations of exons 2 and 3, encoding for the α1 and α2 domains, respectively, of human CD1A, ‐B, ‐C and ‐D genes. We analyzed genomic samples of unrelated, healthy individuals from different ethnic background: 70 Caucasians from Europe, 33 Black Africans (13 from Tanzania and 20 Zulus), 19 Caucasians from the Sahara and 44 Asian individuals. We have found CD1A to be a biallelic locus with a common allele which was present in the majority of the individuals studied. The second allele differed from the common one by a single‐point mutation, resulting in a change of Cys to Trp at position 52 in the α1 domain. This second allele was found in heterozygosis in 7 out of 70 Caucasians from Europe (allelic frequencies P=0.95 and q=0.05). In the Chinese population, we found the second allele present in heterozygosis in 19 from the 44 individuals studied, and we also found 6 homozygous individuals for the second allele (allelic frequencies P=0.64 and q=0.35). In addition, we detected a synonymous mutation (C to T transition) in codon 34 of CD1C exon 2 in 4 out of 20 Zulus and in 2 of the 13 Blacks from Tanzania.
Identification of a novel HLA‐DQA1 allele (DQA1*0106) by sequence‐based DQA1 typing
Authors: Luo M. , Blanchard J. , Maclean I. , Brunham R.
Published: March 2003

We report here a novel DQA1 allele (DQA1*0106) identified during sequence‐based HLA‐DQA1 typing. Polymerase chain reaction with proofreading pfu DNA polymerase and subsequent sequencing yielded identical results as that with Taq DNA polymerase. Molecular cloning and sequencing confirmed that the new DQA1 allele is identical to DQA1*01021/2 at exon 2 except for a single nucleotide substitution (ACT→GCT), changing codon 44 from Thr to Ala. This is the first report of polymorphism at codon 44 of HLA‐DQA1 alleles
Note.
High‐resolution sequence typing of HLA‐DQA1 and ‐DQB1 exon 2 DNA with taxonomy‐based sequence analysis (TBSA) allele assignment
Authors: Luo M. , Blanchard J. , Pan Y. , Brunham K. , Brunham R.c.
Published: March 2003

High‐resolution DNA sequencing of exon 2 of DQA1 and DQB1 genes that uses a taxonomy‐based sequence analysis (TBSA) method to assign alleles was developed. The system uses fewer primers for polymerase chain reaction (PCR) amplification and sequencing than other methods and yields accurate DQA1 and DQB1 typing when either homozygous or heterozygous DNA samples are tested. The approach was initially corroborated by the correct typing of 10 blinded samples that had been previously typed by PCR using sequence‐specific oligonucleotide probes (PCR‐SSOP) or serology, and subsequently confirmed by sequencing of cloned PCR products. DNA from peripheral blood cell samples of 130 individuals enrolled in a case‐control analysis of HLA determinants of abdominal aortic aneurysm were subsequently evaluated. Overall, 8 different DQA1 and 19 DQB1 alleles were identified. All 21 DQA1 heterozygous combinations and 45 of 49 DQB1 heterozygous combinations were successfully resolved with TBSA. The two pairs of heterozygous DQB1 combinations that were not unambiguously typed required sequence specific PCR amplification for correct allele identification. We conclude that the method provides precise analysis for HLA‐DQ typing.
A gene telomeric of the HLA class I region is involved in predisposition to both type 1 diabetes and coeliac disease
Authors: Lie B.A. , Sollid L.M. , Ascher H. , Ek J. , Akselsen H.E. , Rønningen K.S. , Thorsby E. , Undlien D.E.
Published: March 2003

We have recently shown that an as yet unidentified gene within or in the vicinity of the HLA complex, in linkage disequilibrium with microsatellite D6S2223, modifies the risk to develop type 1 diabetes independently of HLA‐DR and ‐DQ genes. This microsatellite is located 2.5 Mb telomeric to HLA‐F and particular alleles at this microsatellite modifies the risk encoded by the high‐risk DRB1*03‐DQA1*0501‐DQB1*0201 (hereafter called DR3) haplotype. Coeliac disease and type 1 diabetes share some susceptibility HLA class II haplotypes, in Scandinavia particularly the DR3 haplotype. We therefore investigated whether the marker D6S2223 might also be associated with coeliac disease. In order to keep the contributions from the DRB1‐DQA1‐DQB1 genes constant (i.e., eliminate the effects of linkage disequilibrium to disease associated DR and/or DQ alleles), we only used cases and controls being homozygous for DR3. We found the frequency of allele 3 at D6S2223 to be reduced among patients with coeliac disease compared to controls, to a similar extent as seen in type 1 diabetes, which could not be explained by a different distribution of HLA‐B alleles (as ascertained by typing for the MIB microsatellite). This negatively associated allele 3 at D6S2223 occurred in a homozygous combination at a significantly lower frequency among patients than controls. Thus, allele 3 at D6S2223 on DR3 haplotypes is associated with reduced susceptibility for development of both type 1 diabetes and coeliac disease. This suggests that a gene(s) in the vicinity of D6S2223 is involved in the pathogenesis of both of these immune‐mediated diseases
Nomenclature for factors of the dog major histocompatibility system (DLA), 1998. First report of the ISAG DLA Nomenclature Committee
Authors: Kennedy L.J. , Altet L. , Angles J.M. , Barnes A. , Carter S.D. , Francino O. , Gerlach J.A. , Happ G.M. , Ollier W.E.R. , Polvi A. , Thomson W. , Wagner J.L.
Published: March 2003

A Nomenclature Committee for factors of the dog major histocompatibility system or dog leukocyte antigen (DLA) has been convened under the auspices of the International Society for Animal Genetics (ISAG) to define a sequence‐based nomenclature for the genes of the DLA system. The remit of this committee includes: i) assignment of gene names; ii) rules for naming alleles; iii) assignment of names to published alleles; iv) assignment of names to new alleles; and v) rules for acceptance of new alleles.
Characterisation of a novel HLA‐A pseudogene, HLA‐BEL, with significant sequence identity with a gorilla MHC class I gene
Authors: Williams F. , Curran M.D. , Middleton D.
Published: March 2003

During the development of an HLA‐A polymerase chain reaction using sequence‐specific oligonucleotide probes (PCR‐SSOP) method for the identification of HLA‐A*24 and ‐A*30 alleles, group amplification resulted in the formation of an unusual PCR product in certain individuals. This fragment was approximately 900 bp smaller than the expected product and was also detected in some non‐HLA‐A*24‐ and ‐A*30‐positive individuals acting as negative controls for the group specific amplification. Nucleotide sequence analysis of this product identified it as a unique class I gene sequence displaying homology to both primate and human class I A‐locus genes. The entire gene was amplified using PCR and the complete DNA sequence information from exon 1 to exon 8, including introns, was determined. A recombination event was identified which results in the fusion of intron 2 with intron 3, causing a deletion of the intervening exon 3 sequence. In addition, there are two cytosine insertions in the poly‐cytosine stretch at the start of exon 4 which cause a frameshift and premature termination. The exon 1 and 2 sequences most closely align with the gorilla allele A*0501, displaying only five mismatches. PCR analysis has established that the gene is associated with the following HLA‐A types: HLA‐A*3001, ‐A*3301, ‐A*3303, ‐A*6802, ‐A*2901, ‐A*0203, ‐A*0205 and ‐A*31012. Reverse transcription (RT)‐PCR analysis of individuals containing this gene failed to detect any mRNA transcription, suggesting that this is a previously undescribed non‐expressed class I pseudogene which we have provisionally named HLA‐BEL. Its unique gene structure gives a possible insight into the evolutionary pathway that created HLA class I genes.
Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan) supports the premise that they descent from Upper Paleolithic populations of East Asia
Authors: Bannai M. , Ohashi J. , Harihara S. , Takahashi Y. , Juji T. , Omoto K. , Tokunaga K.
Published: March 2003

Acknowledgments:

We thank Prof. Masafumi Takiguchi, Kumamoto University, Dr. Marie Lau, UCLA, and Mr. Hiromitsu Takei, Japanese Red Cross Ibaraki Blood Center, for providing us with standard genomic clones and standard genomic DNAs. We also thank Dr. Tadashi Imanishi, Mr. Hidenori Tanaka, Mr. Kouichi Kashiwase, and Dr. Atsuko Ogawa, Japanese Red Cross Central Blood Center, for helpful discussions. This study was partially supported by Grant‐in‐Aid for Scientific Research on Priority Areas from the Ministry of Education, Science, Sports and Culture.

The Ainu people are assumed to be the descendants of pre‐agricultural native populations of northern Japan, while the majority of population of present‐day Japan (Hondo‐Japanese) is considered to have descended mainly from post‐neolithic migrants. Sequence‐level polymorphisms of the HLA‐class I (HLA‐A and HLA‐B) genes were investigated in DNA samples of 50 Ainu living in Hidaka district, Hokkaido. HLA‐A*2402, A*0201, A*0206, A*2601, A*3101, B*1501, B*5101, B*3901, and B*3501 were observed at frequencies of more than 10% and most of these have previously been found in populations of not only Asians but also North and South American Indians. A*68012, which has not so far been detected in Hondo‐Japanese, was found in the Ainu (3%). On the other hand, several alleles common in Hondo‐Japanese, including HLA‐A*3303, A*1101, B*4403, B*5201, B*5401, B*4601, and B*0702 were infrequent in Ainu (0–1%). Correspondence and neighbor‐joining analyses of various populations based on HLA‐A, ‐B and ‐DRB1 gene frequencies enabled distinction between Asian, Native South American, European, and African populations. The Ainu, as well as Tlingit (Na‐Dene), were placed midway between other East Asians, including Hondo Japanese, and Native South Americans (Amerindians) in the correspondence analysis. Furthermore, several HLA‐A‐B and HLA‐B‐DR‐DQ haplotypes common in the Ainu, are shared with some Native American populations. These observations strongly suggest a unique place for the Ainu as descendants of some Upper Paleolithic populations of East Asia, from whom some Native Americans may have descended.
On the MICA deleted‐MICB null, HLA‐B*4801 haplotype
Authors: Ota M. , Bahram S. , Katsuyama Y. , Saito S. , Nose Y. , Sada M. , Ando H. , Inoko H.
Published: March 2003

A 100‐kb deletion including the MICA gene was recently reported in the HLA‐B48 (B*4801)‐associated haplotype in Japanese. Interestingly, this MICA deletion is accompanied by a MICB null allele, MICB0107N. In order to further investigate the universality of the apparent tight linkage between these two events, we present data on high‐resolution deletion mapping of eight HLA‐B48‐homozygous individuals. Among these, five carried the MICA deletion linked to MICB0107N, as originally reported. Conversely, the remaining three possessed an intact MICA gene of MICA008 or MICA010 allelic variant associated this time with a putative expressed MICB allele, MICB0102. These results may imply that the expression of both MICA and MICB molecules is indispensable to viability through a yet‐to‐be understood mutual interaction in immune surveillance.
HLA class II alleles in Japanese patients with immune thrombocytopenic purpura. Associations with anti‐platelet glycoprotein autoantibodies and responses to splenectomy
Authors: Kuwana M. , Kaburaki J. , Pandey J.P. , Murata M. , Kawakami Y. , Inoko H. , Ikeda Y.
Published: March 2003

HLA class II alleles and immunoglobulin allotypes were determined in 83 Japanese patients with immune thrombocytopenic purpura (ITP) and 114 race‐matched healthy controls. Distribution of DRB and DQB1 alleles as well as G1M(f, z), G2M(n+, n−), and KM(1, (1,2), 3) were not different between ITP patients and healthy controls, while DPB1*0201 was marginally increased in ITP patients vs. healthy controls (51% vs. 28%, Pc=0.04, OR=2.6 [1.4–4.8]). In contrast, strong associations between anti‐glycoprotein autoantibodies and HLA class II genes were found as follows: anti‐GPIIb‐IIIa antibody with DRB1*0405 and DQB1*0401; and anti‐GPIb‐IX antibody with DRB1*0803 and DQB1*0601. When factors influencing therapeutic responses to splenectomy were examined, a poor response was correlated with the presence of DRB1*0405, DQB1*0401 and anti‐GPIIb‐IIIa antibody (P=0.01, 0.002, and 0.03, respectively). Our results indicate that HLA class II genes influence the production of anti‐glycoprotein antibody specificities rather than the development of ITP. In addition, HLA class II genotyping could be useful in predicting therapeutic responses to splenectomy in Japanese patients with ITP.
HLA‐DRB1 DNA sequencing based typing: an approach suitable for high throughput typing including unrelated bone marrow registry donors
Authors: Sayer D. , Whidborne R. , Brestovac B. , Trimboli F. , Witt C. , Christiansen F.
Published: March 2003

The HLA‐DRB1 sequencing based typing strategies reported to date require separate amplifications of each sample with a series of group‐specific primers followed by sequencing of any resulting polymerase chain reaction (PCR) products. Whilst this results in high resolution typing in the majority of cases, a number of unnecessary amplifications are performed. We report here a novel approach where amplification of the second exon of HLA‐DRB1 is performed in a single tube for all alleles. Retrospective analysis of 642 consecutive Western Australian unrelated bone marrow registry donors has shown that this approach results in unambiguous typings in 71.1% of cases. Ambiguities can be readily resolved if necessary with a single additional sequencing reaction on the original PCR product.
HLA‐B allele frequencies in Côte d’Ivoire defined by direct DNA sequencing: identification of HLA‐B*1405, B*4410, and B*5302
Authors: Ellis J.M. , Hoyer R.J. , Costello C.N. , Mshana R.N. , Quakyi I.A. , Mshana M.N. , Diaby B. , Traore M. , Johnson A.H. , Hurley C.K.
Published: March 2003

Abstract: Direct automated DNA sequencing was used to analyze exons 2 and 3 of HLA‐B alleles present in forty‐four unrelated individuals residing in the village of Adiopodoume, Côte d’Ivoire (Ivory Coast). Of the 23 HLA‐B alleles observed, the most frequently detected allele was HLA‐B*5301 (22.7%), which is believed to confer resistance to severe Plasmodium falciparum malaria. B*4501 (9.1%), B*1503 (8.0%), B*0705 (5.7%), B*1510 (5.7%) and B*3501 (5.7%) occurred frequently in the population. A second allele of B53 was identified; B*5302 contains a single amino acid variation at residue 171 (Y→H). Two additional novel alleles, B* 1405 (a single amino acid variant of B*1402) and B*4410 (a five amino acid variant of B*4403) were characterized.
CD1 genotyping of patients with Mycobacterium malmoense pulmonary disease
Authors: Jones D.C. , Gelder C.M. , Ahmad T. , Campbell I.A. , Barnardo M.C.N.M. , Welsh K.I. , Marshall S.E. , Bunce M.
Published: March 2003

Abstract: Mycobacterium malmoense is an opportunistic mycobacterium that occasionally causes disease in non‐immunosuppressed individuals. As only a few individuals exposed to these organisms actually develop clinical disease, it is possible there is a genetic component to susceptibility. CD1 molecules are capable of presenting antigens from more virulent mycobacteria to T cells; therefore, we were interested in discovering whether recently described polymorphisms in CD1 molecules modulated susceptibility to M. malmoense pulmonary disease. The CD1 system comprises five genes (CD1A, ‐B, ‐C, ‐D, and ‐E) located on chromosome 1 (1q22–23). CD1 molecules are structurally and functionally related to major histocompatibility complex (MHC) class I molecules and are expressed on dedicated antigen‐presenting cells. The primary function of CD1 molecules is to present lipid and glycolipid antigens to T cells. We have developed an allele‐specific polymerase chain reaction‐sequence‐specific primer (PCR‐SSP) method of CD1 genotyping. Using this method, we compared the allele and haplotype frequencies of CD1 in 49 HIV‐negative patients with M. malmoense pulmonary disease with those in 342 normal controls. The CD1A and CD1E alleles were nominally identified as CD1A*01, CD1A*02, CD1E*01 and CD1E*02, and the control gene frequencies were found to be 5%, 95%, 67% and 33%, respectively. No significant difference was observed between the patient and control cohorts. Positive linkage disequilibrium values of 0.73 were observed between CD1A*02 and CD1E*01 (P<0.0001; χ2 test), and 0.94 between CD1A*01 and CD1E*02 (P<0.0001; χ2 test). Typing was also performed for two previously described CD1D alleles (CD1D*01 and CD1D*02), although only CD1D*01 was detected.
Linkage disequilibria between HLA‐B, C1_4_1, MICA and MICB
Authors: Glas J. , Werner A.I. , Brünnler G. , Witter K. , Scholz S. , Weiss E.H. , Albert E.D.
Published: March 2003

Abstract:The polymorphisms of MICA exon 5 (5 alleles), MICB intron 1 (13 alleles), C1_4_1 (6 alleles), HLA‐B (29 alleles) and HLA‐A (15 alleles) were investigated in a healthy German population. Sequencing was performed for the MICB alleles CA14, CA15, CA17, CA23 and CA26 isolated from different cell lines. Variation to the published sequence was observed for CA14, CA15 and for CA17. At the C1_4_1 locus a new allele (CAAA)9was identified and confirmed by sequencing. Linkage disequilibria were investigated for two‐point‐ and three‐point‐haplotypes. Although the average relative delta value correlates loosely with the physical distance from HLA‐B to MICB: HLA‐B–C1_4_1>HLA‐B–MICA>HLA‐B–MICB, there are several exceptions to this rule. Analyzing three‐point‐haplotypes for the segment MICB to HLA‐A a wide variation of linkage disequilibria for some of the classical HLA‐A, B haplotypes has been observed. While the HLA‐A1, B8 haplotype displays strong relative delta values over the entire distance from HLA‐A to MICB, other haplotypes have linkage disequilibria only in a limited region.
Identification of a novel gp100/pMel17 peptide presented by HLA‐A*6801 and recognized on human melanoma by cytolytic T cell clones
Authors: Sensi M. , Pellegatta S. , Vegetti C. , Nicolini G. , Parmiani G. , Anichini A.
Published: March 2003

Abstract: Melanoma‐associated peptides recognized by cytolytic T lymphocytes (CTL) in the context of several histocompatibility leukocyte antigens (HLA) are required for the development of specific immunotherapies. Using a transient transfection assay into COS‐7 cells, we identified the gp100/pMel17 melanosomal protein as the shared antigen recognized by three independent CD8+ CTL clones in HLA‐A*6801‐restricted fashion. This finding was confirmed by the correlation between lack of gp100/pMel17 protein in a number of HLA‐A*6801‐positive melanomas and their resistance to lysis/cytokine production by the specific effectors. The gp100/pMel17 antigenic epitope was identified based on recognition of subfragments and on a computer‐based prediction algorithm. Among a panel of gp100/pMel17‐derived synthetic peptides only the 10‐mer HTMEVTVYHR (gp100/pMel17182−191) induced tumor necrosis factor (TNF) release by CTL clones when pulsed on suitable target cells whereas both the 10‐mer and the shorter 9‐mer gp100/pMel17183−191 sensitized the same antigen‐pulsed cells to lysis. In conclusion, the identification of the HTMEVTVYHR peptide will extend to HLA‐A*6801 melanoma patients the possibility to exploit gp100/pMel17 melanosomal protein for experimental and clinical studies.
Simultaneous genotyping of single nucleotide polymorphisms in the IL‐6, IL‐10, TNFα and TNFβ genes
Authors: Tseng L.‐H. , Chen P.‐J. , Lin M.‐T. , Singleton K. , Martin E. G. , Yen A.‐H. , Chuang S.‐M. , Martin P.J. , Hansen J.A.
Published: March 2003

Abstract: Single nucleotide polymorphisms (SNP) in the human IL‐6, IL‐10, TNFα and TNFβ genes have been associated with gene function and susceptibility to disease. In this study, primers containing mismatches at 1–3 nucleotide positions were designed to incorporate a new restriction site recognized by endonucleases AlwNI, BcgI, BglI, BsaBI, BslI, BstXI, EcoNI or XcmI for genotyping SNPs in the IL‐6 gene (position − 174), IL‐10 gene (positions −592 and −1082), TNFα gene (positions −238, − 308 and −863) and TNFβ gene (position + 249) by mismatched polymerase chain reaction and restriction fragment length polymorphism (PCR/RFLP). Our results show that appropriately designed BslI‐based mismatched PCR/RFLP assays can be successfully used to determine the genotypes for approximately 40% of SNPs. The mismatched PCR strategy can be coupled with multiplex‐amplification to enable simple and rapid determination of several SNP genotypes in a single reaction.
TNFα−308A associated with shorter intervals of Plasmodium falciparum reinfections
Authors: Meyer C.G. , May J. , Luty A.J. , Lell B. , Kremsner P.G.
Published: March 2003

Abstract: A mutation at position −308 of the tumor necrosis factor α (TNF−308A) gene promoter has previously been associated with particular manifestations of infectious and non‐infectious diseases. In a longitudinal study on malariological parameters in Gabon, TNF promoter variants of 98 children initially presenting with severe Plasmodium falciparum malaria, followed by a total of 504 reinfection events within 52 months, and 100 children initially presenting with mild malaria followed by a total of 342 reinfections were analyzed. Symptomatic P. falciparum reinfections occurred more quickly (median 11 weeks) in carriers of the TNF−308A allele, with severe malaria at enrollment, compared to carriers of other TNF promoter variants (median 16 weeks). The results show that this particular TNF promoter allele increases the risk of reinfection with the malaria parasite P. falciparum.
NKT cells: Potential targets for autoimmune disease therapy?
Authors: Hammond K.J.L. , Godfrey D.I.
Published: March 2003

Abstract: NKT cells represent a unique T cell lineage that recognize glycolipid antigens in the context of the non‐classical MHC class I molecule CD1d. NKT cells are potent producers of immunoregulatory cytokines, and have been implicated in several different autoimmune diseases in mice and humans, including Type 1 diabetes, experimental autoimmune encephalomyelitis – a mouse model for multiple sclerosis, systemic lupus erythematosus, and scleroderma. This review will cover the evidence for an involvement for NKT cells in these autoimmune diseases, and discuss the potential for therapeutic manipulation of these cells as a means of preventing autoimmune disease in the clinic.
Analysis of HLA in children with gelatin allergy
Authors: Sakaguchi M. , Nakayama T. , Kaku H. , Taniguchi K. , Saito S. , Kimura A. , Inouye S.
Published: March 2003

Abstract: Systemic immediate reactions including anaphylaxis to gelatin in vaccines have been reported. However, the number of such reports is very small compared with the number of children exposed to gelatin. The present study was designed to investigate whether susceptibility or resistance to gelatin allergy is associated with human leukocyte antigen (HLA) class II gene. Blood samples were obtained from 49 patients with gelatin allergy and specific IgE to gelatin. DNA‐based HLA class II typing was performed to determine the DRB1, DQB1 and DPB1 alleles. Genotype frequencies were compared with those found in 240 unrelated controls. The frequency of DQB1*0303 (55.1%) was significantly higher in the patients than in the control subjects (32.1%). The frequency of DPB1*0402 was also significantly higher in the patients (32.7%) than in the control subjects (15.4%). On the other hand, the frequency of subjects carrying DRB1*15 (DRB1*1501 and DRB1*1502) was significantly lower among the patients group (18.4%) than among the controls (40.8%). We found that DQB1*0303 and DPB1*0402 were positively associated with the IgE response for gelatin, while DRB1*15 was negatively associated with it.
A MAGE‐3 peptide presented by HLA‐B44 is also recognized by cytolytic T lymphocytes on HLA‐B18
Authors: Bilsborough J. , Panichelli C. , Duffour M‐T. , Warnier G. , Lurquin C. , Schultz E.S. , Thielemans K. , Corthals J. , Boon T. , Van Der Bruggen P.
Published: March 2003

Abstract: Antigens encoded by MAGE genes are of particular interest for cancer immunotherapy because of their tumoral specificity and because they are shared by many tumors. Antigenic peptide MEVDPIGHLY, which is encoded by MAGE‐3 and is known to be presented by human leukocyte antigen (HLA)‐B44, is currently being used in therapeutic vaccination trials. We report here that a cytolytic T lymphocyte (CTL) clone, which is restricted by HLA‐B*1801, recognizes the same peptide and, importantly, lyzes HLA‐B18 tumor cells expressing MAGE‐3. These results imply that the use of peptide MEVDPIGHLY can now be extended to HLA‐B18 patients. We also provide evidence that, under limiting amounts of protein MAGE‐3, HLA B*1801 and B*4403 compete for binding to the peptide.
Synthesis and characterization of a series of novel glutamic γ‐15N‐anilide dipeptides
Authors: Huang X. , Day N. , Luo X. , Roupioz Y. , Seid M. , Keillor J.W.
Published: March 2003

The preparation of a series of novel Cbz–Gln–Gly dipeptide derivatives is reported, wherein the γ‐carboxamide groups of the glutamine side chains have been modified to γ‐15N‐anilides which are substituted in the para position with ‐NO2, ‐Cl, ‐H, ‐CH3, ‐OCH3, and ‐N(CH3)2. Characterization of the free anilines (pKa values and 15N NMR chemical shifts) and corresponding γ‐anilides (15N NMR chemical shifts and FTIR wavenumbers) is also reported. Correlation of these physicochemical data to Hammett substituent parameters (σpara) is discussed. These novel dipeptide derivatives should prove to be generally useful for structure–function enzymology studies of γ‐glutamyl transferring enzymes.
Design of synthetic hexapeptide substrates for prostate‐specific antigen using single‐position minilibraries
Authors: Yang C.F. , Porter E.S. , Boths J. , Kanyi D. , Hsieh M.‐C. , Cooperman B.S.
Published: March 2003

Abstract: Prostate‐specific antigen (PSA), a serine endoprotease with chymotrypsin‐like substrate specificity, is a marker used widely for detection of prostate cancer and other prostate diseases, catalyzing hydrolysis of the gel‐forming proteins semenogelins I and II, which are synthesized and secreted by the seminal vesicle. In this study we report the use of two single‐position minilibraries and RP‐HPLC selection to optimize a hexapeptide substrate for PSA, spanning substrate positions P3 to P3′. PSA has been shown previously to prefer tyrosine in position P1[Denmeade et al. (1997) Cancer Research,57, 4924–4930]. Here we demonstrate preference for serine in position P1′ and strong preference for phenylalanine in position P2. Based on these results we have designed and demonstrated the utility of the optimized fluorogenic PSA substrate 7‐methoxy‐coumarin‐4‐acetylGlnPheTyrSerSerAsnLys(ε‐2,4‐dinitrophenyl)amide, I, which permits continuous monitoring of PSA endopeptidase activity at high sensitivity.
Preferred conformations of a linear RGD tripeptide
Authors: Kang Y.K. , Jhon J.S.
Published: March 2003

Abstract: Conformational study of RGD tripeptides in the nonhydrated and hydrated states was carried out using an empirical potential function ECEPP/3 and the hydration shell model in order to investigate preferred conformations and factors responsible for their stability. RGD tripeptides in the nonhydrated and hydrated states can be interpreted as existing as an ensemble of feasible conformations rather than as a single dominant conformation from the analysis of distributions of backbone conformations, hydrogen bonds and β‐turns. The different distributions of conformations for the neutral and zwitterionic RGD tripeptides in both states may indicate that the conformation of the RGD tripeptide is liable to depend on solvent polarity and pH values. β‐Turn populations for the neutral tripeptide in both states are reasonably consistent with NMR measurements on linear RGD‐containing peptides. The degradation of RGD tripeptide seems to be attributed mainly to the hydrogen bonds between the Asp side‐chain and the backbone of Asp residue or C‐terminal NHMe group, rather than to the flexible backbones of Gly and Asp residues.
Caution in the use of 2‐iminothiolane (Traut's reagent) as a cross‐linking agent for peptides. The formation ofN‐peptidyl‐2‐iminothiolanes with bombesin (BN) antagonist (d‐Trp6,Leu13‐ψ[CH2NH]‐Phe14)BN6−14andd‐Trp‐Gln‐Trp‐NH2
Authors: Mokotoff M. , Mocarski Y.M. , Gentsch B.L. , Miller M. , Zhou J.‐H. , Chen J. , Ball E.D.
Published: March 2003

Abstract:During a study aimed at generating a bispecific molecule between BN antagonist (d‐Trp6,Leu13‐ψ[CH2NH]‐Phe14)BN6‐14(Antag1) and mAb22 (anti‐FcγRI), we attempted to cross‐link the two molecules by introducing a thiol group into Antag1 via 2‐iminothiolane (2‐IT, Traut's reagent). We found that reaction of Antag1 with 2‐IT, when observed using HPLC, affords two products, but that the later eluting peptide is rapidly transformed into the earlier eluting peptide. To understand what was occurring we synthesized a model peptide,d‐Trp‐Gln‐Trp‐NH2(TP1), the N‐terminal tripeptide of Antag1. Reaction of TP1 with 2‐IT for 5 min gave products1aand3a; the concentration of1adecreased with reaction time, whereas that of3aincreased. Thiol1a, the expected Traut product, was identified by collecting it in a vial containingN‐methylmaleimide and then isolating the resultant Michael addition product2a, which was confirmed by mass spectrometry. Thiol1ais stable at acidic pH, but is unstable at pH 7.8, cyclizes and loses NH3to giveN‐TP1‐2‐iminothiolane (3a), ES‐MS (m/z) [602.1 (M+H)+], as well as regenerating TP1. Repeat reaction with Antag1 and 2‐IT allowed us to isolateN‐Antag1–2‐iminothiolane (3b), FAB‐MS (m/z) [1212.8 (M+H)+] and trap the normal Traut product1bas itsN‐methylmaleimide Michael addition product2b, ES‐MS (m/z) [1340.8 (M+H)+]. Thiol1bis also stable at acidic pH, but when neutralized is unstable and cyclizes, forming3band Antag1.
Insect neuropeptide antagonist. Part II. Synthesis and biological activity of backbone cyclic and precyclic PBAN antagonists
Authors: Zeltser I. , Bhargava K. , Gilon C. , Ben‐Aziz O. , Schefler I. , Altstein M.
Published: March 2003

Abstract:A new approach for the design and synthesis of pheromone biosynthesis activating neuropeptide (PBAN) agonists and antagonists using the backbone cyclization and cycloscan concepts is described. Two backbone cyclic (BBC) libraries were synthesized: library I (Ser library) was based on the active C‐terminal hexapeptide sequence Tyr‐Phe‐Ser‐Pro‐Arg‐Leu‐NH2of PBAN1‐33NH2; whereas library II (d‐Phe library) was based on the sequence of the PBAN lead linear antagonist Arg‐Tyr‐Phe‐d‐Phe‐Pro‐Arg‐Leu‐NH2. In both libraries the Pro residue was replaced by the BBC building unit Nα‐(ω‐aminoalkyl) Gly having various lengths of alkyl chain. The peptides of the two libraries were tested for agonistic and antagonistic activity. Four precyclic peptides based on two of the BBC antagonists were also synthesized; their activity revealed that a negative charge at the N‐terminus of the peptide abolished antagonistic activity. We also describe the use of the reagent SiCl3I for selective deprotection of the Boc group from the building unit prior to on‐resin amino‐end to backbone‐nitrogen (AE‐BN) cyclization, during solid‐phase synthesis with Fmoc chemistry.
Novel peptide inhibitors for Grb2 SH2 domain and their detection by surface plasmon resonance
Authors: Lung F.‐D. T. , Tsai J.‐Y. , Wei S.‐Y. , Cheng J.‐W. , Chen C. , Li P. , Roller P. P.
Published: March 2003

Abstract: One of the critical intracellular signal transduction pathways involves the binding of the Grb2 SH2 domain to the phosphotyrosine (pTyr) motifs on growth factor receptors, such as epidermal growth factor receptor (EGFR) and erbB2, leading to downstream activation of the oncogenic Ras signaling pathway. Therefore, the Grb2 SH2 domain has been chosen as our target for the development of potential anticancer agents. As a continuation of our earlier work, herein we report the design and synthesis of new peptide analogs, and their inhibitory effect on the Grb2 SH2 domain using surface plasmon resonance (SPR) technology. These novel agents do not contain phosphotyrosine or phosphotyrosine mimics. Binding interactions between these peptides and the Grb2 SH2 domain were measured and analyzed using a BIAcore X instrument, which provides detailed information on the real‐time detection of the binding interaction. The results of this study should provide important information for the further development of peptides or peptidomimetics with high affinity for the Grb2 SH2 domain.
Synthetic peptide epitope‐based polymers: controlling size and determining the efficiency of epitope incorporation
Authors: Sadler K. , Zeng W. , Jackson D.C.
Published: March 2003

Abstract: The assembly of synthetic peptide‐based vaccines that incorporate multiple epitopes is a major goal of vaccine development, because such vaccines will potentially allow the immunization of outbred populations against a number of different pathogens. We have shown that free radical‐induced polymerization of individual peptide epitopes results in the incorporation of multiple copies of the same or different epitopes into high molecular weight immunogens (O'Brien‐Simpson, N.M., Ede, N.J., Brown, L.E., Swan, J. & Jackson, D.C. (1997) Polymerization of unprotected synthetic peptides: a view toward synthetic peptide vaccines. J. Am. Chem. Soc.119, 1183–1188; Jackson, D.C., O'Brien‐Simpson, N., Ede, N.J. & Brown, L.E. (1997) Free radical induced polymerization of synthetic peptides into polymeric immunogens. Vaccine15, 1697–1705). The ability to control the size of these polymers, to determine the physical and chemical properties of the backbone material and also to know the extent to which individual peptide epitopes are incorporated are important manufacturing considerations and form the subject of this study. We show here that the polymerization process is highly efficient with at least 70% of peptides incorporated into the resulting polymer, that acrylamide and acryloylated amino acids can be used as comonomers with peptide epitopes in the polymerization reaction and that the choice of the comonomer can influence the properties of the resulting polymer. We also show that the size of chain growth polymers is restricted in the presence of chain transfer agents, that the resulting polymer size can be predicted and that there is little or no difference in the immunogenicity of polymers that range in apparent molecular size between 18 kDa and 335 kDa. The successful polymerization of peptide epitopes with an acryloyl‐amino acid creates the potential for introducing different physical and chemical properties into artificial protein immunogens.
Structure−antigenicity relationship studies of the central conserved region of human respiratory syncytial virus protein G
Authors: Sugawara M. , Czaplicki J. , Ferrage J. , Milon A. , Haeuw J.‐F. , Power U. F. , Corvaïa N. , Nguyen T. , Beck A.
Published: March 2003

Abstract: BBG2Na is a recombinant protein, composed in part of carrier protein BB and of the central conserved domain of the attachment glycoprotein G of human respiratory syncytial virus (HRSV) subgroup A. This protein is a potent vaccine candidate against HRSV. G2Na contains several contiguous B‐cell epitopes, occupying sequential positions in the linear sequence of the protein. One of the epitopes contains four cysteines that are completely conserved in known strains of HRSV and form a ‘cysteine noose’ motif. In this study, we analysed circular dichroism (CD) spectra of BBG2Na and its B‐cell epitopes. We also used NMR and molecular dynamics simulations to determine the three‐dimensional structure of the cysteine noose domain. We observed significant structural differences related to the length of peptides containing the cysteine noose. These differences show good correlation with the immunogenic activity of the peptides. It is shown that a single Val171 addition induces a pronounced structure stabilization of the cysteine noose peptide G4a (1–4/2−3) (residues 172–187), which is associated with a 100‐fold increase in its antigenicity vis‐à‐vis a G‐protein specific monoclonal antibody.
Studies on the aggregation and possible channel formation in membranes of a cyclic hexapeptide, cyclo (d‐Ala‐l‐Pro‐l‐Ala)2
Authors: Ramesh J. , Ghosh J.K. , Swaminathan C.P. , Ramasamy P. , Surolia A. , Sikdar S.K. , Easwaran K.R.K.
Published: March 2003

Abstract: The interaction of zwitterionic lipid DMPC and DPPC with cyclic hexapeptide, cyclo (d‐Ala‐l‐Pro‐l‐Ala)2 was studied using circular dichroism (CD) and differential scanning calorimetry (DSC). Preliminary membrane conductance results showed that the peptide has a tendency to form channels inside the lipid bilayer. CD studies indicated that as the lipid/peptide (L/P) ratio (DMPC/peptide) was increased, the magnitude of the negative CD band having a λmax around 200 nm decreased. At a L/P ratio of 210:1, this band disappeared completely, indicating dramatic conformational changes in the peptide on interaction with the lipid bilayer. Reduction of the phase transition temperature and the maximum heat capacity of the lipid bilayer (DPPC) for gel‐to‐liquid crystalline phase transition indicates a strong interaction of the peptide with the lipid bilayer.
Circular dichroism and Fourier transform infrared spectroscopic studies on self‐assembly of tetrapeptide derivative in solution and solvated film
Authors: Ganesh S. , Jayakumar R.
Published: March 2003

Abstract:  Aggregation of the hydrophobic peptide derivative Boc‐Ala‐Ile‐Ile‐Gly‐OMe (1) was examined in methanol solution and in solvated film states. Formation of the peptide by self‐assembly was evidenced using fluorescence [Mg salt of 8‐anilino‐naphthalenesulfonic acid (ANS) as an external probe] and circular dichroism (CD) spectroscopic techniques. In solution, peptide 1 formed as a stable aggregate at a concentration around 3 × 10−4m. The peptide gelled into a thin film for which we carried out CD and Fourier transform infrared (FTIR) measurements. Our spectroscopic study on peptide films at differing methanol concentrations indicates that the helical content of the peptide decreases with decreasing methanol concentration in solvated films. However, by reducing the methanol concentration we were able to observe a conformational transition from a predominantly helical turn to a β‐sheet structure via a random coil conformation. Our study focused on the aggregation of the α‐helical turn‐forming peptide derivative, which shows conformational transition on changing solvent concentration in the film form.
Purification of two depressant insect neurotoxins and their gene cloning from the scorpion Buthus martensi Karsch
Authors: Wang C‐G. , Ling M‐H. , Chi C‐W. , Wang D‐C. , Stankiewicz M. , Pelhate M.
Published: March 2003

Abstract:  Insect‐specific neurotoxins are important components of scorpion venoms. In this study, two toxins from the scorpion Buthus martensi Karsch (BmK) were purified. They shared high sequence homology with other depressant insect toxins and were designated BmK ITa and BmK ITb, respectively. They were able to suppress the action potential of cockroach isolated axon, which is due to a decrease in the peak sodium current. Furthermore, the effect of BmK ITb was lower than that of BmK ITa, and some of the electrophysiological characteristics of BmK ITb even resemble that of excitatory insect toxins. Their primary structures were determined by N‐terminal partial sequence determination and cDNA cloning. The differences in their structures, especially the 31st residues, may result in the unique activity of BmK ITb.
Peptides corresponding to the N‐ and C‐terminal parts of PEBP are well‐structured in solution: new insights into their possible interaction with partners in vivo
Authors: Vallée B.S. , Coadou G. , Labbé H. , Sy D. , Vovelle F. , Schoentgen F.
Published: March 2003

Abstract:  Recently, it has been shown that mammalian PEBPs are implicated in several signalling pathways controlling the cellular cycle. In particular, during brain development, the N‐terminal part of mammalian PEBP is specifically cleaved and the resulting 11 amino acid peptide stimulates the growth and activity of acetylcholinergic neurons. The crystallographic structure of bovine and human PEBPs has revealed that their N‐ and C‐terminal parts are accessible and exposed to the solvent suggesting that they may be involved in specific interactions with cellular partners. We have chemically synthetized the two peptides corresponding to these terminal parts and studied their structure in solution by circular dichroism and NMR spectroscopies: both of them are well‐structured. The N‐terminal peptide is composed of a series of turns, leading to a hook conformation. The C‐terminal peptide displays a globally helical conformation similar to that observed in the whole protein; it is characterized by an amphipatic feature with a hydrophobic cluster located on one side. These structural features enlighten previous fluorescence and monolayer experiments and give new insights on the roles of both PEBP termini.