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PubMed1993

HLA DPB1 genotyping in Australian aborigines by amplified fragment length polymorphism analysis.

The HLA-DPB1 alleles in 93 Australian aborigines, from two geographically separate areas within Australia, were studied by AFLP analysis. There was a restricted range of DPB1 alleles seen in the aboriginal population, and the distribution of alleles varied between the two aboriginal groups. DPB1*0501 was the most common allele in the aborigines from the Central Desert, whereas DPB1*0401 was the most frequent allele in the Northern Coast aborigines. A new AFLP pattern was observed, and was found to correspond to the allele DPB1*2201, recently identified by SSO analysis. The DPB1 allele frequency distribution for both of the aboriginal groups was different from that seen for the Australian Caucasoid population.

Alleles↗
PubMed1996

[Study on some susceptible genes of systemic lupus erythematosus in Han nationality of China].

In order to explore the allelic polymorphism of HLA-DR and TNF B loci and susceptibility to systemic lupus erythematosus (SLE) in the Han nationality of northern China with the aid of methods of polymerase chain reaction/sequence specific primers (PCR/SSP) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) respectively. The findings from a case-control study on 151 blood samples (45 from the cases and 106 from the controls) indicated that there were significantly higher frequency of DR2 (P < 0.05, RR = 1.56) and DR3 (P < 0.01, RR = 2.69), which represent candidate susceptible genes or useful markers for SLE. The DR5 allele in the samples (P < 0.05, RR = 0.43) might be an antagonistic or protective allele, or a marker for such allele. The frequency of TNF B * 1 and TNF B * 2 alleles was investigated in 45 SLE patients and 80 healthy controls and it was found that the frequency of TNF B * 2 allele was significantly higher in the patient group (P < 0.05, RR = 1.84). It might also be a suspicious susceptible allele or a marker for such allele. The frequency of HLA polymorphisms in various clinical/immunological subsets of our patient population was also determined. Clinical findings used include plasma SC5b-9 level, SSA, SSB, Sm, RNP, ANA antibodies, and SLE complications (SLE nephritis, pneumonia & encephalopathy). It turned out that there was a positive association between HLA-DR2 allele and SLE nephritis (P < 0.05, RR = 1.32).

Alleles↗
PubMed1994

Intracellular transport of class I HLA molecules is affected by polymorphic residues in the binding groove.

Intracellular transport of class I MHC complexes is dependent on assembly of class I heavy chains with beta 2-microglobulin (beta 2m) and peptides. This suggests that amino acid residues of individual class I molecules which are important for their stability and transport are likely to include those which contribute to binding of a majority of the cleft-associated peptides. To identify such critical residues, substitutions at polymorphic positions within the peptide binding cleft were introduced into a mutant HLA-A*0201 molecule bearing an additional gly > lys substitution at position 242 (242K). The 242K mutation weakens association of the HLA-A*201 heavy chain with beta 2m and was used to enhance potential effects of substitutions in the peptide binding groove on class I stability. Critical in choosing which binding cleft positions to mutate was the observation that HLA-A*6801 was less sensitive to the effects of 242K mutation than HLA-A*0201 and A*6901. This suggested that one or more of the six residues in the alpha 2 domain differing between HLA-A*6901 and A*6801 were likely to affect class I complex stability. Positions 95, 97, 107, 114, 116, and 156 in either 242K or wild-type HLA-A*0201 molecules were therefore each converted to those residues found in HLA-A*6801. One of the second-site substitutions, arg > met at position 97, increased stability and restored surface expression of the 242K molecule. Five other substitutions either had no additional effect or further impaired 242K stability. Substitution of his > arg at position 114 blocked surface expression of both 242K and wild-type HLA-A*0201 molecules. These results demonstrate that polymorphic residues in the binding cleft influence the stability of class I complexes, and suggest that position 97 plays a critical role in stabilizing class I molecules for transport.

Binding Sites↗
PubMed2005

[Determination of HLA-A, B, and DRB1 gene polymorphism in Monba ethnic group of Xizang Autonomous Region, China].

OBJECTIVE: To investigate the HLA-A, B, DRB1 allele polymorphism in Monba ethnic population of Xizang Autonomous Region. METHODS: HLA-A, B, DRB1, DNA types in 47 unrelated Monba ethnic healthy individuals from the Xizang Autonomous Region of China were analyzed by polymerase chain reaction-based reverse line-strip sequence specific oligonucleotide hybridization. Based on the HLA-DRB1 alleles frequencies of 11 other ethnic groups in China, a molecular phylogenetic tree was constructed by the Neighbor-Joining (NJ) method. RESULTS: Twenty-three alleles were detected for HLA-A, 39 for HLA-B, and 33 for HLA-DRB1. HLA-A*1101, A*2402, A*02011, A*0206, HLA-B*3802, B*4001, B*4002, B*51011, HLA-DRB1*12021, DRB1*0403, DRB1*0701, DRB1*1201 were the most common alleles. The most frequent alleles were HLA-A*1101(0.2128), HLA-B*3802(0.1064), and HLA-DRB1*12021(0.0851). CONCLUSION: The HLA loci are highly polymorphic in Monba population of Xizang Autonomous Region. Compared with other ethnic groups in China, the Monba ethnic group is close to Tibetan ethnic group.

Alleles↗
PubMed1995

HLA class I variation in Australian aborigines: characterization of allele B*1521.

Traditional methods of serological typing have largely used antisera of Caucasoid origin, which can overlook HLA heterogeneity in non-Caucasoid populations. Therefore, we have used molecular techniques to evaluate potential polymorphism in HLA class I molecules of Aborigines from the central desert and northern coast of Australia. The DNA sequence of common Aboriginal HLA-A and B antigens were compared with serological reaction patterns which suggested new polymorphisms. Although serological data indicated that long and short variants of A34 may exist, regardless of the serological pattern, all individuals carried the A*3401 allele. Therefore, the variation in A34 reaction pattern observed serologically was not attributable to primary sequence variation in the HLA A*3401 allele. Similarly, there was no detectable polymorphism in the sequences of selected HLA-B alleles, even though some of these alleles showed unusual serological reaction patterns. However, a new allele of B15 (B*1521) was detected in two individuals carrying this serotype. The cells from both of these individuals showed ambiguous reaction patterns with monospecific B62 and B75 sera. cDNA sequencing of the HLA B15 gene from these cells revealed a B15 allele that differed from B*1502 by a single nucleotide change. This change occurred at position 272, resulting in a C to G substitution at residue 67 in the consensus B15 cDNA sequence. Hence, the Australian Aborigines as an ethnic group show very little primary sequence polymorphism within the class I loci, consistent with the results obtained from previous serological studies.

Amino Acid Sequence↗
PubMed1993

Lack of disease associated HLA-DQ restriction fragment length polymorphisms in families with autoimmune thyroid disease.

Autoimmune thyroid disease (AITD) is often familial and serological HLA disease associations have been described in many different populations. However, such HLA disease associations are weak and the precise molecular contribution of HLA antigens to thyroid disease susceptibility remains unknown. Much of the data available are cross-sectional and few studies have explored familial inheritance of AITD at the molecular level. We have, therefore, examined the inheritance of AITD in multiplex and multi-generational families using restriction fragment length polymorphism (RFLP) analysis of DNA digested with the restriction enzyme BamH1 and probed with a full length human HLA-DQ beta cDNA probe. Thirty seven subjects in 7 informative families were available for study. Eleven subjects had Graves' disease and 4 were diagnosed as having Hashimoto's thyroiditis. Segregation of polymorphic fragments enabled genotyping of each individual to produce fully informative families. LOD scores were computed, using the LIPED program, for dominant and recessive models of inheritance, for recombination fractions of 0.01 to 0.5 for each sex, and for penetrances of 0.1 to 1.0. The results showed that maximum LOD scores were negative for all of the inheritance models tested. If the primary locus for AITD were in the HLA region, LOD scores would be highly positive. These data, therefore, provide strong evidence against a disease locus for AITD in linkage disequilibrium with the HLA-DQ beta locus.

Adult↗
PubMed1996

HLA-DRB1, DQA1, DQB1 DNA polymorphism in the Bulgarian population.

We describe for the first time the use of PCR based techniques to analyze the MHC class II polymorphism of the Bulgarian population. The present study provides the HLA-DRB, DQB1 allele frequencies in 116 Bulgarian individuals and DQA1 alleles frequencies in 100 subjects. DNA from these individuals was typed for DRB and DQB1 typed by the PCR-Allele Specific Amplification (PCR-ASA) method and DQA1 by PCR followed by hybridization using Sequence Specific Oligonucleotides (PCR-SSO). Allele and haplotype frequencies and linkage disequilibria are computed by the standard methods used for the XIth International Histocompatibility Workshop. The highest frequencies are 0.159, 0.109 and 0.085 for DRB1*1101, DRB1*1601 and DRB1*1301 respectively. Among the eight DQA1 alleles detected, DQA1*0501 (0.344) is found to be much more frequent than the two most frequent alleles DQA1*0102 (0.225) and DQA1*0101 (0.151). Twelve DQB1 alleles are found and three of them, DQB1*0301 (0.280), DQB1*0502 (0.153) and DQB1*0201 (0.133) showed the highest frequencies. The haplotype DRB1*1101-DQA1*0501-DQB1*0301 (0.079) predominate clearly, followed by DRB1*1601-DQA1*0102-DDQB1*0502 (0.055) and DRB1*0101-DQA1*0101-DQB1*0501. These results indicate that the Bulgarian population is characterized by features representative of the European anthropological type with a substantial contribution from the Southern Belt of Europe.

Alleles↗
PubMed1997

Preferential presentation of herpes simplex virus T-cell antigen by HLA DQA1*0501/DQB1*0201 in comparison to HLA DQA1*0201/DQB1*0201.

The HLA DQA1 locus is polymorphic. Haplotypes containing HLA DQA1*0501, but not HLA DQA1*0201, together with HLA DQB1*0201 are associated with Grave's disease and celiac sprue. In this report, we demonstrate a functional correlate of DQA1 polymorphism. T cells infiltrating a herpes simplex virus (HSV) lesion from a HLA DQ 2,7 individual yielded a virus-specific CD4+ clone restricted by DQ2. Presentation of viral peptide and protein segregated with DQA1 allele, because cell lines bearing DQA1*0501/DQB1*0201 heterodimers presented antigen in proliferation and cytotoxicity assays much more efficiently than cell lines bearing DQA1*0201/DQB1*0201. Binding of viral peptide to cell lines bearing DQA1*0201, in comparison to DQA1*0501, was only moderately reduced and may not explain this effect. Truncation and substitution analyses of peptide binding and T-cell activation were performed to determine which viral peptide residues contacting TCR might therefore be presented in an altered conformation by DQA1*0201/DQB1*0201. Residues 432, 435, 437, 438, and 440 (position P1, P4, P6, P7, and P9) contributed to DQ2 binding, whereas residues 431, 433, 434, and 436 (positions P 1, P2, P3, and P5) contributed to TCR contact. Differential presentation of peptide by HLA DQ2 heterodimers varying at the DQA1 locus may have relevance to host defense and the pathogenesis of HLA DQ2-associated autoimmune diseases.

Alleles↗
PubMed1989

CD4+ cytolytic T cell clones restricted to HLA class II, DR beta I, and DR beta III chains.

We have investigated the functional polymorphism of HLA class II antigens using CD4+ CTL clones. Seven CD4+ CTL clones were isolated from a healthy donor (HLA A2 A24; B8 B27; DRw17 DRw52a) by repeated stimulation with irradiated autologous EBV-transformed B cell lines (EBV-B). According to the HLA restriction specificity we divided CD4+ CTL clones into three subgroups: (i) DRw17-restricted CD4+ CTL clones; (ii) DRw52a-restricted CD4+ CTL clones; and (iii) the CD4+ CTL clones, of which the restriction specificity could not be assigned to products of a single HLA locus. Interestingly, DRw17-restricted CD4+ CTL clones distinguished between DRw17 and DRw18. Similarly, DRw52a-restricted CD4+ CTL clones distinguished between DRw52a, w52b, and w52c. There are four amino acids which differ between DRw17 and DRw18, whereas five differ between DRw52a and the other two alleles (DRw52b and DRw52c). The recent elucidation of the crystal structure of a human class I MHC molecule has identified the probable peptide binding site to be a cleft on the outer surface of the molecule, between two alpha-helices. On the basis of the theoretical model for HLA class II molecules, amino acid positions 26 and 28 (DRw17 vs DRw18) and amino acid positions 26, 28, and 74 (DRw52a vs the other two alleles) lie within the "cleft." We propose that amino acid positions 26 and 28 are very important sites with regard to the recognition of antigen-MHC complex by the TCR.

Binding, Competitive↗
PubMed2006

[The analysis of HLA-A, B and DRB1 allelic polymorphism in Han race population in Lanzhou region of China].

OBJECTIVE: To investigate the HLA-A, B and DRB1 allele polymorphism of the Han race population in Lanzhou area. METHODS: Polymerase chain reaction-sequence specific primer was used to detect HLA-A, B and DRB1 alleles in 200 unrelated healthy Han individuals from Lanzhou region, Northwest China, and the results were compared with those of Han populations in North, South and Northwest China, and Hui, Uigur and Tibetan population in China. RESULTS: Fourteen of alleles were detected and identified for HLA-A; 32 for HLA-B; and 13 for HLA-DRB1. HLA- A*01, A*02,A*11,A*24, A*30, A*31, A*33; HLA- B*13, B*15, B*40, B*44, B*46, B*51, B*58, B*60; HLA- DRB1*04,. DRB1*07, DRB1*08, DRB1*09, DRB1*11, DRB1*12, DRB1*14 and DRB1*15 were the most common alleles. The frequencies of HLA-A, B and DRB1 genes of Lanzhou Han race were close to that of North China Hans and Hui population in Northwest China, and a little different to that of South China Hans. The HLA-DRB1 alleles were significantly different to those of Uigur and Tibetan race population of China. CONCLUSION: The allelic polymorphism of HLA-A,B and DRB1 loci of Han race population in Lanzhou area was between North and South Han race of China, close to Northwest China Hui, and markedly different to Northwest China Uigur and Tibetan race populations.

Adult↗
PubMed2001

Distribution of HLA-A, B alleles and polymorphisms of TAP and LMP genes in Korean patients with atopic dermatitis.

BACKGROUND: Atopic dermatitis has been seen to result from multifactorial inheritance, with interaction between genetic and environmental factors. The genetic association may differ according to the ethnic backgrounds. OBJECTIVE: The purpose of this study was to investigate the genetic factors in Korean atopic dermatitis patients by studying the human leucocyte antigen (HLA) class I association and polymorphisms of transporters associated with antigen presentation (TAP) and low-molecular-weight polypeptide (LMP) genes. METHODS: HLA-A and B genotyping was performed in 53 atopic dermatitis patients and 184 healthy controls using the standard microlymphocytotoxicity technique. TAP1, TAP2, LMP2, and LMP7 gene polymorphisms were anaylzed using the polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP), PCR-amplification refractory mutation system (ARMS), and PCR-restriction fragment length polymorphism (RFLP). RESULTS: Allele frequency of HLA-A24 was significantly increased in patients with atopic dermatitis compared to controls (P < 0.05). HLA-B alleles showed no differences in distribution between patients and controls. Genotype, phenotype, and allele frequencies of TAP1 gene also revealed no differences in distribution between patients and controls. Analysis of TAP2 gene polymorphisms showed increased frequencies of the TAP2*C allele and TAP2*A/TAP2*C genotype in atopic dermatitis patients compared to controls (P < 0.05). Distribution of LMP2 and LMP7 gene polymorphisms was similar for patients and controls. CONCLUSION: This study demonstrates an association of atopic dermatitis with HLA-A24 and TAP2*C alleles in Korean patients. Discrepancy with the previous reports might be related to different patient characteristics and ethnic variations.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1990

T-cell receptor beta-chain DNA polymorphism frequencies in healthy HLA-DR homozygotes.

In view of numerous recent reports of T-cell receptor (TCR) beta-chain/disease associations with HLA-associated diseases, we tested the possibilities that associations might exist directly between these two gene complexes at the level of the germline DNA. We determined frequencies of five TCR-beta DNA polymorphisms in 33 HLA-DR2/2 homozygotes, 29 HLA-DR3/3 homozygotes and 42 HLA-DR4/4 homozygotes. The control population (n = 74) was chosen without "bias toward" their HLA-DR genes. We selected DR2, DR3 and DR4 homozygotes because they have been the most frequently involved in HLA-DR associated diseases. Our results indicate that the recent reports in the literature of TCR-beta/disease associations can not be explained by a significantly different distribution of TCR-beta genes in HLA-DR2+, -DR3+, or -DR4+ subpopulations. Our results also suggest that if co-evolution between TCR-beta and MHC haplotypes does exist, the selective pressures in recent generations have not been strong enough to significantly alter the germline TCR-beta gene frequencies in HLA-DR2+, -DR3+, or -DR4+ subpopulations.

Alleles↗
PubMed1999

The DRB1 Val86/Val86 genotype associates with multiple sclerosis in Australian patients.

Genetic susceptibility to multiple sclerosis (MS) has so far been strongly localized to the MHC class II region encoding the alleles of the haplotype HLA-DRB1*1501, -DQA1*0102, -DQB1*0602. However, this haplotype is not carried by approximately 40% of MS patients; a potential explanation could be that they carry other MHC class II alleles with similar function due to the sharing of nucleotide sequences encoding critical amino acid residues. The DRB1 gene is polymorphic at residue 86, encoding valine or glycine. In view of the increasing evidence for a functional role for DRB1 aa86 in the binding and presentation of autoantigenic peptides such as myelin basic protein, this study investigated associations with the residue 86 polymorphism in an Australian MS population. A significant increase in the Val86/Val86 genotype was observed in the MS patients, which was still present in the absence of the DRB1*1501 allele (p = 0.032). This suggest that DRB1 aa86 may have an independent role in contributing to MS susceptibility. The Val86/Val86 genotype was correlated with genotyping for other putative MS susceptibility genes, including T cell receptor beta chain germline polymorphisms, HLA-DMB alleles, and -DQA1 and -DQB1 alleles encoding critical amino acid residues, with a significant interaction only observed with DQB1 Leu26 (p = 0.014). Additional studies of the HLA-DRB1 aa86 polymorphism in MS, and its function, are needed to more fully understand this association.

Alleles↗
PubMed1991

HLA-DRB nucleotide sequences arranged in polymorphic groups.

The nucleotide sequence information of HLA-DR B genes is presented in this short review in a format which is useful for designing sequence specific oligonucleotides (SSOs) for DNA typing. The relationships between various HLA-DR alleles are also shown.

Base Sequence↗
PubMed2003

Polymorphism of intron 4 in HLA-A, -B and -C genes.

The sequence database of HLA class I genes focuses on the coding sequences, the exons. Limited information is available on the non-coding sequences of the different class I alleles. In this study we have determined the intron 4 nucleotide sequence of at least one representative of each major allelic group of HLA-A, -B and -C. The intron 4 sequences were determined for 27 HLA-A, 81 HLA-B and 30 HLA-C alleles by allele-specific sequencing, using primers located in adjacent exons and introns. The sequences revealed that the length of intron 4 varies with a minimum of 93 and a maximum of 124 nucleotides as a result of insertions and deletions. There were remarkable similarities and differences within HLA-A, -B and -C, as well as between them. Within HLA-A, a deletion of three nucleotides was detected in several HLA-A alleles. The HLA-B alleles could be divided into two groups with one group having a deletion of 11 nucleotides compared with the second group. Within HLA-C, all Cw*07 alleles showed remarkable differences with the other Cw alleles. Cw*07 had an insertion of three nucleotides, shared only by the Cw*17 group. Moreover, Cw*07 was found to have an aberrant nucleotide sequence. Differences between HLA-A, -B and -C alleles were also observed. Remarkable was the deletion of 20 nucleotides in all HLA-A and -B alleles compared with HLA-C, whereas the HLA-A alleles showed an insertion of one nucleotide and a deletion of three nucleotides compared with HLA-B and -C. Furthermore, 32 different polymorphic positions were detected between HLA-A, -B and -C.

Alleles↗
PubMed1998

HLA-A*24-B*07-DRB1*01 haplotype implicated with genetic disposition of peak bone mass in healthy young Japanese women.

HLA exhibits the most extensive polymorphism of any of the known human genes and is known as a genetic marker which allows genetic background of many diseases and physical phenomena. In this study, we, therefore, tried to investigate the regulation of HLA polymorphism and peak bone mass (PBM) in order to elucidate the genetic backgrounds of bone metabolism in young women. Subjects were 67 healthy young Japanese women (average age: 23.6 +/- 2.6 years, Body Mass Index (BMI): 19.9 +/- 2.0 who were randomly chosen. Allelic polymorphisms in HLA class I (HLA-A and -B) and HLA-class II (DRB1) were investigated by PCR-SSOP and PCR-SSP. Vitamin D Receptor (VDR) and Estrogen Receptor (ER) gene polymorphisms were also analyzed. Lifestyle factors, such as exercise and nutrition, were examined by questionnaire. Bone mineral density was examined using with Lunar DPX-L. Subjects who possessed HLA-B*07 had a significantly lower PBM than those without B*07 (p < 0.05). All subjects were divided into 3 groups according to HLA haplotypes linked with HLA-B*07, as follows: A*24(+/-)B*07(-)DRB1*01(+/-), A*24(+)B*07(+)DRB1*01(-), and A*24(+)B*07(+)DRB*01(+). There were no significant differences between these three groups in factors that affect bone metabolism, such as age, age at menarche, BMI, calcium intake, exercise habits, VDR or ER allele frequency. The HLA-A*24-B*07-DRB1*01 haplotype had a significantly lower Z score in the lumbar spine compared with subjects without this haplotype (p < 0.05). When the Z score was divided by values higher or lower than +1 or -1, all 3 subjects whose Z score was lower than -1.0 were found to have the HLA-A*24-B*07-DRB1*01 haptotype. A significant association between HLA-A*24-B*07-DRB1*01 and Z score < -1 was found (Yate's correction chi(2) = 10.82, p = 0.001, RR = 204). In conclusion, the HLA-A*24-B*07-DRB*01 haplotype can be considered a new genetic marker implicated with low PBM in healthy young Japanese women.

Adult↗