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Fernando MMA, Freudenberg J, Lee A, Morris DL, Boteva L, Rhodes B, Gonzalez-Escribano MF, Lopez-Nevot MA, Navarra SV, Gregersen PK, Martin J, Vyse TJ. Transancestral mapping of the MHC region in systemic lupus erythematosus identifies new independent and interacting loci at MSH5, HLA-DPB1 and HLA-G. Ann Rheum Dis 2012; 71:777-84. [PMID: 22233601 PMCID: PMC3329227 DOI: 10.1136/annrheumdis-2011-200808] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Objectives Systemic lupus erythematosus (SLE) is a chronic multisystem genetically complex autoimmune disease characterised by the production of autoantibodies to nuclear and cellular antigens, tissue inflammation and organ damage. Genome-wide association studies have shown that variants within the major histocompatibility complex (MHC) region on chromosome 6 confer the greatest genetic risk for SLE in European and Chinese populations. However, the causal variants remain elusive due to tight linkage disequilibrium across disease-associated MHC haplotypes, the highly polymorphic nature of many MHC genes and the heterogeneity of the SLE phenotype. Methods A high-density case-control single nucleotide polymorphism (SNP) study of the MHC region was undertaken in SLE cohorts of Spanish and Filipino ancestry using a custom Illumina chip in order to fine-map association signals in these haplotypically diverse populations. In addition, comparative analyses were performed between these two datasets and a northern European UK SLE cohort. A total of 1433 cases and 1458 matched controls were examined. Results Using this transancestral SNP mapping approach, novel independent loci were identified within the MHC region in UK, Spanish and Filipino patients with SLE with some evidence of interaction. These loci include HLA-DPB1, HLA-G and MSH5 which are independent of each other and HLA-DRB1 alleles. Furthermore, the established SLE-associated HLA-DRB1*15 signal was refined to an interval encompassing HLA-DRB1 and HLA-DQA1. Increased frequencies of MHC region risk alleles and haplotypes were found in the Filipino population compared with Europeans, suggesting that the greater disease burden in non-European SLE may be due in part to this phenomenon. Conclusion These data highlight the usefulness of mapping disease susceptibility loci using a transancestral approach, particularly in a region as complex as the MHC, and offer a springboard for further fine-mapping, resequencing and transcriptomic analysis.
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Affiliation(s)
- Michelle M A Fernando
- Division of Genetics and Molecular Medicine and Division of Immunology, Infection and Inflammatory Disease, King's College London, Guy's Hospital, Great Maze Pond, London SE1 9RT, UK.
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2
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Kirk AD, Elster EA. Immunology of Transplantation. Surgery 2008. [DOI: 10.1007/978-0-387-68113-9_81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Fortes MDP, Machado IV, Gil G, Fernández-Mestre M, Dagher L, León RV, Bianco NE, Tassinari P. Genetic contribution of major histocompatibility complex class II region to type 1 autoimmune hepatitis susceptibility in Venezuela. Liver Int 2007; 27:1409-16. [PMID: 17927716 DOI: 10.1111/j.1478-3231.2007.01581.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
AIMS Autoimmune hepatitis (AIH) is a progressive liver disease characterized by the presence of circulating autoantibodies, hypergammaglobulinaemia and a favourable response to immunosuppressive treatment. Although the pathogenesis of type 1 AIH is unknown, disease susceptibility is partially determined by genes linked to the class II region of the major histocompatibility complex. Type 1 AIH has been associated with DRB1*03, DRB1*04 and DRB3 alleles in European and North American Caucasians, with DRB1*0405 in Japanese, with DRB1*0404 in Mexican, and with DRB1*1301 in Argentinean populations. METHODS To analyse the molecular basis of these associations in Venezuela (mestizo population), we examined the frequency of human leucocyte antigens (HLA)-A -B -C, HLA-DQ and HLA-DR genes by low- and high-resolution oligonucleotide typing in a population of 41 type 1 AIH patients and 111 ethnic- and aged-matched healthy subjects. RESULTS The frequencies of both DRB1(*)1301 (P<0.0001) and DRB1*0301 (P<0.005) were significantly higher in patients than in controls. In addition, patients showed a strong association with the DRB3 allele (P<0.01). In contrast, the DQB1*04 allele was significantly decreased in the patient group (P<0.01). The frequencies of haplotypes A*01-B*08-DQB1*02-DRB1*03-DRB3, DQB1*05-DRB1*1301, DQB1*06-DRB1*1301 and A*02-DRB1*1301, B*45-DRB3 were significantly increased in type 1 AIH patients compared with the controls (P<0.01). CONCLUSIONS In conclusion, our data indicate that type 1 AIH predisposition in a Venezuelan mestizo population of different ethnic backgrounds is associated with DRB1*1301 and DRB1*0301 alleles. In addition, our findings suggest that protection against disease might be conferred by the DQB1*04 allele, with distinct ethnic differences from other populations.
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4
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Miterski B, Drynda S, Böschow G, Klein W, Oppermann J, Kekow J, Epplen JT. Complex genetic predisposition in adult and juvenile rheumatoid arthritis. BMC Genet 2004; 5:2. [PMID: 15018649 PMCID: PMC356909 DOI: 10.1186/1471-2156-5-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2003] [Accepted: 02/04/2004] [Indexed: 11/29/2022] Open
Abstract
Background Rheumatoid arthritis (RA) and juvenile rheumatoid arthritis (JRA) are complex multifactorial diseases caused by environmental influences and an unknown number of predisposing genes. The present study was undertaken in order to investigate association of polymorphisms in candidate genes with RA and JRA in German subjects. Results Up to 200 unrelated German RA and JRA patients each and 300–400 healthy controls have been genotyped for HLA-DRB1, TNFa, TNFA -238a/g, TNFA -308a/g, TNFA -857c/t, TNFR1 -609g/t, TNFR1 P12P, TNFR2 del 15bp, IKBL -332a/g, IKBL -132t/a, IKBL C224R, CTLA4 -318c/t, CTLA4 T17A, PTPRC P57P, MIF -173g/c, the MIF and IFNG microsatellites as well as for D17S795, D17S807, D17S1821 by polyacrylamide gel electrophoresis, single-strand conformation polymorphism analysis, restriction fragment length polymorphism analysis or allele specific hybridization. None of the investigated genetic markers is associated with both, RA and JRA, but there are some statistically significant differences between patients and controls that have to be discussed sensibly. Conclusions The difficulty in investigating the genetics of complex disorders like RA and JRA may arise from genetic heterogeneity in the clinically defined disease cohorts (and generally limited power of such studies). In addition, several to many genes appear to be involved in the genetic predisposition, each of which exerting only small effects. The number of investigated patients has to be increased to establish the possibility of subdivison of the patients according their clinical symptoms, severity of disease, HLA status and other genetic characteristics.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Adult
- Age of Onset
- Aged
- Alleles
- Antigens, CD/genetics
- Antigens, Differentiation/genetics
- Arthritis, Juvenile/genetics
- Arthritis, Rheumatoid/genetics
- CTLA-4 Antigen
- Child
- DNA/genetics
- Female
- Gene Frequency
- Genetic Predisposition to Disease/genetics
- Genotype
- Germany
- HLA-DR Antigens/genetics
- HLA-DRB1 Chains
- Histocompatibility Antigens Class II/genetics
- Humans
- Interferon-gamma/genetics
- Leukocyte Common Antigens/genetics
- Macrophage Migration-Inhibitory Factors/genetics
- Male
- Microsatellite Repeats/genetics
- Middle Aged
- Polymorphism, Genetic
- Polymorphism, Single-Stranded Conformational
- Receptors, Tumor Necrosis Factor/genetics
- Receptors, Tumor Necrosis Factor, Type I
- Receptors, Tumor Necrosis Factor, Type II
- Tumor Necrosis Factor-alpha/genetics
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Affiliation(s)
- Bianca Miterski
- Department of Human Genetics, Ruhr-University Bochum, Germany
| | - Susanne Drynda
- Department of Rheumatology, University Hospital, Magdeburg, Germany
| | - Gundula Böschow
- Department of Pediatrics, Carl-Thiem-Hospital, Cottbus, Germany
| | - Wolfram Klein
- Department of Human Genetics, Ruhr-University Bochum, Germany
| | | | - Jörn Kekow
- Department of Rheumatology, University Hospital, Magdeburg, Germany
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Katunuma N, Matsunaga Y, Himeno K, Hayashi Y. Insights into the roles of cathepsins in antigen processing and presentation revealed by specific inhibitors. Biol Chem 2003; 384:883-90. [PMID: 12887055 DOI: 10.1515/bc.2003.099] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Eleven human cathepsins have been identified, however, the in vivo roles of individual cathepsins are still largely unknown. In this brief review we will summarize the functions of individual cathepsins in antigen processing and presentation, which are the initial steps of the immune response. Two general inhibitors of papain-like cysteine proteases, E-64 and pyridoxal phosphate, can completely suppress antigen presentation in vivo. To evaluate the contribution of individual cathepsins, specific inhibitors have been developed based on cathepsin tertiary structures: CA-074 for cathepsin B, CLIK-148 and -195 for cathepsin L, CLIK-60 for cathepsin S. Administration of CA-074, a cathepsin B inhibitor, suppresses the response to exogenous antigens, such as hepatitis B virus antigen, ovalbumin and Leishmania major antigen, and induces switching of the helper T cell responses from Th-2 to Th-1 of CD4+ T cells, thereby downregulating the production of IgE and IgG1. Administration of the cathepsin S inhibitor CLIK-60 impairs presentation of an autoantigen, alpha-fodrin, in Sjogren's syndrome and suppresses the Th-1 response and autoantibody production.
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Affiliation(s)
- Nobuhiko Katunuma
- Tokushima Bunri University, Institute for Health Sciences, Tokushima 770-8514, Japan
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6
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Kawamura K, Yamamura T, Yokoyama K, Chui DH, Fukui Y, Sasazuki T, Inoko H, David CS, Tabira T. Hla-DR2-restricted responses to proteolipid protein 95-116 peptide cause autoimmune encephalitis in transgenic mice. J Clin Invest 2000; 105:977-84. [PMID: 10841661 PMCID: PMC377477 DOI: 10.1172/jci8407] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In multiple sclerosis (MS) patients who carry the Class II major histocompatibility (MHC) type HLA-DR2, T cells specific for amino acids 95-116 in the proteolipid protein (PLP) are activated and clonally expanded. However, it remains unclear whether these autoreactive T cells play a pathogenic role or, rather, protect against the central nervous system (CNS) damage. We have addressed this issue, using mice transgenic for the human MHC class II region carrying the HLA-DR2 (DRB1* 1502) haplotype. After stimulating cultured lymph node cells repeatedly with PLP95-116, we generated 2 HLA-DR2-restricted, PLP95-116-specific T-cell lines (TCLs) from the transgenic mice immunized with this portion of PLP. The TCLs were CD4+ and produced T-helper 1 (Th1) cytokines in response to the peptide. These TCLs were adoptively transferred into RAG-2/2 mice expressing HLA-DR2 (DRG1* 1502) molecules. Mice receiving 1 of the TCLs developed a neurological disorder manifested ataxic movement without apparent paresis on day 3, 4, or 5 after cell transfer. Histological examination revealed inflammatory foci primarily restricted to the cerebrum and cerebellum, in association with scattered demyelinating lesions in the deep cerebral cortex. These results support a pathogenic role for PLP95-116-specific T cells in HLA-DR2+ MS patients, and shed light on the possible correlation between autoimmune target epitope and disease phenotype in human CNS autoimmune diseases.
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Affiliation(s)
- K Kawamura
- Department of Demyelinating Disease and Aging, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
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Escalante AA, Lal AA, Ayala FJ. Genetic polymorphism and natural selection in the malaria parasite Plasmodium falciparum. Genetics 1998; 149:189-202. [PMID: 9584096 PMCID: PMC1460124 DOI: 10.1093/genetics/149.1.189] [Citation(s) in RCA: 186] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We have studied the genetic polymorphism at 10 Plasmodium falciparum loci that are considered potential targets for specific antimalarial vaccines. The polymorphism is unevenly distributed among the loci; loci encoding proteins expressed on the surface of the sporozoite or the merozoite (AMA-1, CSP, LSA-1, MSP-1, MSP-2, and MSP-3) are more polymorphic than those expressed during the sexual stages or inside the parasite (EBA-175, Pfs25, PF48/45, and RAP-1). Comparison of synonymous and nonsynonymous substitutions indicates that natural selection may account for the polymorphism observed at seven of the 10 loci studied. This inference depends on the assumption that synonymous substitutions are neutral, which we test by analyzing codon bias and G+C content in a set of 92 gene loci. We find evidence for an overall trend towards increasing A+T richness, but no evidence for mutation bias. Although the neutrality of synonymous substitutions is not definitely established, this trend towards an A+T rich genome cannot explain the accumulation of substitutions at least in the case of four genes (AMA-1, CSP, LSA-1, and PF48/45) because the Gleft and right arrow C transversions are more frequent than expected. Moreover, the Tajima test manifests positive natural selection for the MSP-1 and, less strongly, MSP-3 polymorphisms; the McDonald-Kreitman test manifests natural selection at LSA-1 and PF48/45. We conclude that there is definite evidence for positive natural selection in the genes encoding AMA-1, CSP, LSA-1, MSP-1, and Pfs48/45. For four other loci, EBA-175, MSP-2, MSP-3, and RAP-1, the evidence is limited. No evidence for natural selection is found for Pfs25.
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Affiliation(s)
- A A Escalante
- Division of Parasitic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, US Public Health Service, Chamblee, Georgia 30341, USA
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8
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Höhler T, Meyer CU, Notghi A, Stradmann-Bellinghausen B, Schneider PM, Starke R, Zepp F, Sänger R, Clemens R, Meyer zum Büschenfelde KH, Rittner C. The influence of major histocompatibility complex class II genes and T-cell Vbeta repertoire on response to immunization with HBsAg. Hum Immunol 1998; 59:212-8. [PMID: 9568796 DOI: 10.1016/s0198-8859(98)00014-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonresponsiveness to HBsAg vaccination is observed in 5-10% of vaccine recipients and is possibly caused by a defect in the T helper cell compartment. The immune response to HBsAg is influenced by genes of the major histocompatibility complex. We have investigated MHC class I and class II antigens in 53 adult responders and 73 nonresponders. Results obtained in this first study were tested in a second study with 56 responders and 62 nonresponders from an infant vaccination trial. In addition, the peripheral Vbeta-chain T-cell receptor repertoire was investigated using monoclonal antibodies and flow-cytometry in 26 adult responders and 38 nonresponders. As previously reported, nonresponsiveness to HBsAg vaccination was associated with DRB1*3 and DRB1*7. In addition, DRB1*13 was significantly increased among vaccine responders (35.2% vs 5.4%;p < 0.0001) suggesting an immune response promoting effect for this allele whereas the closely related allele DRB1*14 was associated with nonresponse in the infant study. There was no evidence for a hole in the T cell receptor Vbeta repertoire. In conclusion, in agreement with results obtained in mice there appears to be a hierarchy of DRB1* genes in the HBsAg immune response. The possible differential association of DRB1*13 and DRB1*14 may allow the identification of differences between responsiveness and nonresponsiveness to a few amino acid differences in the beta1-domain of the class II heterodimer.
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Affiliation(s)
- T Höhler
- I. Department of Internal Medicine, Johannes Gutenberg University Mainz, Germany.
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9
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Boytim ML, Lyu SC, Jung R, Krensky AM, Clayberger C. Inhibition of Cell Cycle Progression by a Synthetic Peptide Corresponding to Residues 65–79 of an HLA Class II Sequence: Functional Similarities but Mechanistic Differences with the Immunosuppressive Drug Rapamycin. THE JOURNAL OF IMMUNOLOGY 1998. [DOI: 10.4049/jimmunol.160.5.2215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
A synthetic peptide corresponding to a region of the α1 α-helix of DQA03011 (DQ 65–79) inhibits the proliferation of human PBL and T cells in an allele-nonspecific manner. It blocks proliferation stimulated by anti-CD3 mAb, PHA-P, and alloantigen, but not by PMA and ionomycin. Substitution of each amino acid with serine shows that residues 66, 68, 69, 71–73, and 75–79 are critical for function. Inhibition of proliferation is long lasting and is not reversible with exogenous IL-2. The peptide can be added 24 to 48 h after stimulation and still block proliferation. The DQ 65–79 peptide does not affect expression of IL-2 or IL-2R; however, IL-2-stimulated proliferation is inhibited. Cell cycle progression is blocked at the G1/S transition, and the activity of cdk2 (cyclin-dependent kinase 2) kinase is impaired by the continued presence of p27. Although these results suggest a mechanism similar to that of rapamycin, the peptide inhibition is not reversed with FK-506, which indicates a distinct mechanism.
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Affiliation(s)
| | | | - Ron Jung
- *Department of Cardiothoracic Surgery and
| | - Alan M. Krensky
- †Division of Immunology and Transplantation Biology/Department of Pediatrics, Stanford University, Stanford, CA 94305
| | - Carol Clayberger
- *Department of Cardiothoracic Surgery and
- †Division of Immunology and Transplantation Biology/Department of Pediatrics, Stanford University, Stanford, CA 94305
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10
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Maffei A, Harris PE, Reed EF, Del Pozzo G, Ciullo M, Suciu-Foca N, Guardiola J. Differential expression of insulin-dependent diabetes mellitus-associated HLA-DQA1 alleles in vivo. Eur J Immunol 1997; 27:1549-56. [PMID: 9209509 DOI: 10.1002/eji.1830270634] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The strong association of HLA-DQ genes with insulin-dependent diabetes mellitus (IDDM) susceptibility is persuasive evidence of their central role in the etiology of this autoimmune disease. Among other possibilities, it has been proposed that an unbalanced expression of IDDM-associated DQA, and/or DQB alleles may lead to alterations in the composition of alpha beta heterodimers and preferential expression of a particular heterodimer on the antigen-presenting cell surface, leading to self-recognition. In this report, we demonstrate the differential expression of DQA1 alleles in vivo, in particular of the two diabetogenic alleles DQA1*0301 and DQA1*0501. Family studies suggest that unequal HLA-DQA1 allele expression in heterozygous individuals is not associated in cis with the HLA-DQA1 gene, but may be affected by trans-acting determinant(s). We also discuss the segregation of this phenotype in IDDM-affected members. Furthermore, we examined historical samples of PBL from an IDDM-affected individual and an HLA-identical unaffected sibling acting in a kidney transplant program as donor and recipient, respectively. This analysis allowed us to establish that unbalanced expression of DQA1*0301 and DQA1*0501 can be induced by microenvironmental conditions. Inducible differential expression of HLA-DQA1 alleles may account for the discordance in the outcome of autoimmune disease in monozygotic twins and HLA-identical siblings.
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Affiliation(s)
- A Maffei
- International Institute of Genetics and Biophysics, CNR, Naples, Italy.
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11
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McCormack JM, Sherman ML, Maurer DH. Quality control for DNA contamination in laboratories using PCR-based class II HLA typing methods. Hum Immunol 1997; 54:82-8. [PMID: 9154462 DOI: 10.1016/s0198-8859(97)00011-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Quality control (QC) in laboratories performing molecular histocompatibility class II typing often includes a polymerase chain reaction (PCR) approach for monitoring DNA contamination. An oligonucleotide primer set was designed, (RBQBf/RBQBr), which is specific for nonpolymorphic regions of the DR-B, DQ-B, and DP-B consensus sequences with an expected PCR product size of 81 bp. RBQBf/RBQBr detected genomic DNA from reference cell lines LWAGS and BM21 (50 to 100 picograms) as well as DR-B, DP-B, and DQ-B amplicon (1 copy). Additionally, RBQBf/RBQBr detected SSP products from routine DR-B and DQ-B typings. Validation studies employing controlled DNA contamination of laboratory surfaces revealed that increasing amounts of wipe test samples (5% to 20% v/v) were inhibitory to the wipe test PCR, whereas lower amounts (1% to 2%), or alternatively, a diluted wipe test sample, increased the sensitivity of the test and optimized the results. Collectively, this study describes a primer set, RBQBf/RBQBr, which detects both genomic DNA and DR-B, DQ-B, or DP-B amplicon and furthermore illustrates the necessity of routine testing for potential inhibitory factors that may be introduced into the wipe test PCR.
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Affiliation(s)
- J M McCormack
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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12
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Blagitko N, O'hUigin C, Figueroa F, Horai S, Sonoda S, Tajima K, Watkins D, Klein J. Polymorphism of the HLA-DRB1 locus in Colombian, Ecuadorian, and Chilean Amerinds. Hum Immunol 1997; 54:74-81. [PMID: 9154461 DOI: 10.1016/s0198-8859(97)00005-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have characterized the DRB1 genotypes in a sample of 64 South American Indians drawn from populations in Chile, Colombia, and Ecuador. No novel DRB1 alleles were found in the total of 17 different alleles characterized, indicating that rapid allelic generation does not occur at the DRB1 loci, in contrast to HLA-B. Comparison between Chilean and Colombian/Ecuadorian samples revealed no major differences in their allelic frequencies. In the combined Amerind sample the HLA-DRB1*0407 and HLA-DRB1*1402 alleles occurred in the highest frequencies (38% and 22%, respectively). Genetic distance measurement showed the HLA-DRB1 frequencies reported here to agree with findings in other Amerind groups. The high frequencies of both HLA-DRB1*0407 and HLA-DRB1*1602 alleles, in conjunction with their absence in Siberian samples, suggest that migratory groups other than Siberians may have been involved in the peopling of the Americas.
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Affiliation(s)
- N Blagitko
- Max-Planck-Institut für Biologic, Abteilung Immungenetik, Tübingen, Germany
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13
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Maffei A, Pozzo GD, Prisco A, Ciullo M, Harris PE, Reed EF, Guardiola J. Polymorphism in the 5' terminal region of the mRNA of HLA-DQA1 gene: identification of four groups of transcripts and their association with polymorphism in the alpha 1 domain. Hum Immunol 1997; 53:167-73. [PMID: 9129975 DOI: 10.1016/s0198-8859(97)83121-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Relative to other loci in the MHC, the HLA-DQ locus exhibits an exceptional degree of polymorphism of both A1 and B1 genes, particularly in the region coding for alpha and beta chains. Diversification of the association between different alpha and beta molecules either in cis or in trans contributes to the structural diversity of the repertoire of cell-surface class II protein's in the population. In addition, structural allelic polymorphisms in the 5' regulatory region of both DQB1 and DQA1 shows several linkage groups with respect to the allelic coding sequence of the respective genes. We describe here the allelic polymorphism in the DQA1 mRNA structure located at the 5' untranslated terminal region. This portion of the mRNA molecule represents, in many genes, a cis-acting regulatory sequence playing a role in the posttranscriptional mechanisms by which gene expression can be modulated. Based on detailed transcriptional analysis, we have been able to define at least four groups of transcripts in DQA1. The mRNA variability was associated with the polymorphism of the second exon of the DQA1 gene, coding for the alpha 1 domain and not with the DNA polymorphism in the 5' regulatory region.
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Affiliation(s)
- A Maffei
- International Institute of Genetics and Biophysics, CNR, Naples, Italy
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14
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Koelle DM, Johnson ML, Ekstrom AN, Byers P, Kwok WW. Preferential presentation of herpes simplex virus T-cell antigen by HLA DQA1*0501/DQB1*0201 in comparison to HLA DQA1*0201/DQB1*0201. Hum Immunol 1997; 53:195-205. [PMID: 9129979 DOI: 10.1016/s0198-8859(97)00034-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
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.
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Affiliation(s)
- D M Koelle
- Department of Medicine, University of Washington, School of Medicine, Seattle, USA
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15
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Epplen C, Jäckel S, Santos EJ, D'Souza M, Poehlau D, Dotzauer B, Sindern E, Haupts M, Rüde KP, Weber F, Stöver J, Poser S, Gehler W, Malin JP, Przuntek H, Epplen JT. Genetic predisposition to multiple sclerosis as revealed by immunoprinting. Ann Neurol 1997; 41:341-52. [PMID: 9066355 DOI: 10.1002/ana.410410309] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study was designed to examine the immunogenetic background predisposing to multiple sclerosis (MS). Three hundred fifty-eight clinically well-characterized MS patients from Germany were investigated and compared to 395 healthy control subjects. Each individual was genotyped for 22 polymorphic markers located within or close to immunorelevant candidate genes including HLA-DRB1*, T-cell receptor (TCR), cell interaction molecules, cytokines, and cytokine receptor genes. Altogether, approximately 17,000 genetic analyses were performed. Patients were grouped according to the course of MS-relapsing-remitting or chronic progressive. Most of the genetic markers were not associated with increased risk or their exact contribution was not clear (e.g., tumor necrosis factor). The relative risks for HLA-DRB1*15+ and DRB1*03+ individuals were 3.64 and 1.42, respectively. In both groups of patients, certain TCRB gene polymorphisms were risk factors. In DRB1*03+ individuals the relative risk was increased (> 22) when a specific TCRBV6S3 allele was also inherited. Furthermore, distinct linkage disequilibria of TCRBV6S1/TCRBV6S3 elements in patients and control subjects strongly suggested an additional risk factor in the TCRBV region for DRB1*15+ individuals. These findings are discussed with respect to the pathogenesis and rational approaches to the therapy of MS.
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Affiliation(s)
- C Epplen
- Department of Molecular Human Genetics, St. Josef Hospital, Göttingen, Germany
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16
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Sanjeevi CB, Höök P, Landin-Olsson M, Kockum I, Dahlquist G, Lybrand TP, Lernmark A. DR4 subtypes and their molecular properties in a population-based study of Swedish childhood diabetes. TISSUE ANTIGENS 1996; 47:275-83. [PMID: 8773316 DOI: 10.1111/j.1399-0039.1996.tb02554.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The aim of this study was to determine the association between childhood insulin-dependent diabetes mellitus (IDDM) and HLA-DR4 subtypes and to test in a population-based investigation whether the DR4 association has an effect independent to that of DQ. First, HLA genotyping identified DR4 in 337/425 (79%) patients and 148/367 (40%) controls (Odds Ratio 5.67; p < 0.01). Second, a total of 14 DR4 subtypes were detected by PCR and sequence specific oligo probes. Only two DR4 subtypes, DRB1*0401 (62% patients and 25% controls; OR 4.95, p < 0.01) and *0404 (16% patients and 10% controls; OR 1.67, p < 0.05) were however positively associated with the disease. These two subtypes were positively associated only when linked to DQB1*0302-DQA1*0301 (DQ8) (56% patients and 14% controls; OR 7.69, p < 0.01; 15% patients and 10% controls; OR 1.55, p < 0.05, respectively). When DRB1*0401 was linked to DQB1*0301-DQA1*0301 (DQ7) (6% patients and 11% controls; OR 0.52, p < 0.05), this DR4 subtypes was negatively associated with IDDM. Third, tests of strongest association allowed the following ranking of alleles or haplotypes DQB1*0302-DQA1*0301 (DQ8) > DQB1*0302 > DRB1*0401 > DRB1*0404 and the association of DRB1*0401 has a significant effect in DQ8 positive IDDM patients. We conclude that the DR4 association with IDDM is secondary to DQ by linkage disequilibrium, which support the role of HLA-DQ as a primary genetic risk factor for IDDM.
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Affiliation(s)
- C B Sanjeevi
- Karolinska Institute, Department of Molecular Medicine, Karolinska Hospital, Stockholm, Sweden
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17
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Rozemuller EH, Tilanus MG. A computerized method to predict the discriminatory properties for class II sequencing based typing. Hum Immunol 1996; 46:27-34. [PMID: 9157086 DOI: 10.1016/0198-8859(95)00075-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Accurate identification of alleles or groups of alleles is obtained using DNA techniques for HLA class II typing. In PCR-SSP and PCR-SSO the typing resolution is dependent on the location of the amplification primers and the number of oligonucleotide probes used for hybridization. These primers are developed based upon the known allele sequences. However, the number of published allele sequences increases rapidly. Periodic reconsideration of the discriminatory properties of the methods used is necessary and often leads to the addition of primers, and an increase of ambiguous genotypes. SBT is a high-resolution class II typing method which utilizes the second exon sequence at all positions for typing. Using a generic amplification and sequencing approach, a limited number of ambiguous heterozygotes can be expected. However, the number of ambiguities is dependent on the location of the primers. These ambiguities can be solved by the use of group-specific primers in either the amplification or sequencing reaction. To identify the applicability of a SBT approach with respect to typing resolution, it is important to identify these ambiguities and develop strategies to solve them. We developed software that predicts the ambiguous heterozygotes, and analyzes their sequences for group specific primers, solving these ambiguities. The location of the primers is considered as well as the use of generic vs group-specific amplification or sequencing reactions. Allele sequences of all class II genes, as accepted by the WHO nomenclature committee for factors of the HLA system and submitted to the EMBL/Genbank databases, are analyzed to define the allelic discrimination level of HLA-DQB1, -DQA1, -DFB1, -DPA1, -DRB1, -DRB3, -DRB4, and -DRB5.
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Affiliation(s)
- E H Rozemuller
- Diagnostic DNA Laboratory, University Hospital, Utrecht, The Netherlands
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18
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Boysen C, Carlson C, Hood E, Hood L, Nickerson DA. Identifylng DNA polymorphisms in humanTCRA/D variable genes by direct sequencing of PCR products. Immunogenetics 1996. [DOI: 10.1007/bf02660060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Johnson AH, Araujo H, Tang TF, Lee KW, Steiner N, Hurley CK. Cellular crossreactivity. Implications for solid organ transplantation matching. Transplantation 1996; 61:643-8. [PMID: 8610394 DOI: 10.1097/00007890-199602270-00021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
This study evaluates the cellular crossreactivity among DR11, DR13, and DR8 molecules using TLC reagents generated in reciprocal priming combinations where the responder and stimulator cells express different microvariants of DR11. The large majority of T lymphocyte clones (TLC) derived from such stimulation detect not only the product of the specific DR11 allele expressed by the stimulator but also detect subsets of DR molecules that span serologic specificities. Thus, TLC generated in response to DR(alpha,beta1*1102) detect DR(alpha,beta1*1103) and products of specific DR13, DR8, DR2 and DR4 alleles. Whereas, TLC generated in response to DR(alpha,beta1*1104) detect DR(alpha,beta1*1101), DR(alpha,beta1*1103), and products encoded by specific DR8 and DR2 but not DR13 or DR4 alleles. Since DR11 microvariants cannot be identified serologically, this type of mismatch certainly occurs frequently between DR11 serologically matched donors and recipients. Particularly affected are populations, such as the African American population, that exhibit extensive HLA diversity and exhibit different frequencies of HLA alleles compared with those of the majority of serologically matched cadaveric donors. Rapid methods of DNA-based HLA typing now makes it feasible to utilize this methodology for allele level identificaiton of recipient and donor alleles. Based on the strength of the alloproliferative responses and on the recognition patterns of the TLC reported here, we suggest that retransplant patients might benefit by excluding subsequent donors expressing DR molecules that in vitro demonstrate strong cellular crossreactivity with DR molecules expressed by the previous donor(s) as well as those DR molecules shared with the previous donor(s). Since such a matching schema has the potential to improve retransplant allograft survival, particularly in patients from minority population groups, it should be evaluated clinically.
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Affiliation(s)
- A H Johnson
- Department of Pediatrics, Georgetown University Medical Center, Washington, DC 20007, USA
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20
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Rozemuller EH, Chadwick B, Charron D, Baxter-Lowe LA, Eliaou JF, Johnston-Dow L, Tilanus MG. Sequenase sequence profiles used for HLA-DPB1 sequencing-based typing. TISSUE ANTIGENS 1996; 47:72-9. [PMID: 8929715 DOI: 10.1111/j.1399-0039.1996.tb02516.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sequencing-based HLA typing (SBT) is a PCR based high resolution HLA typing method in which polymorphic regions of the gene are sequenced and directly used for typing. Currently, for class II SBT, alleles are identified by comparison of the exon 2 sequence with their corresponding allele sequence library. Routine SBT requires reliable identification of heterozygosity, and automated assignment of the alleles. In sequencing strategies different enzymes can be used for primer extension. The most characteristic difference between sequences obtained by two protocols using Sequenaseregistered, or Taq-cycle sequencing, respectively, is a difference in incorporation of nucleotides in the primer extension leading to different sequence profiles. In Taq-cycling sequencing variable nucleotide incorporation results in irregular, but reproducible peak patterns, whereas Sequenase incorporates nucleotides in nearly equal amounts, resulting in more even peak patterns. In a previously published multi-center study we evaluated HLA-DPB1 SBT using Taq-cycle sequencing, and showed that typing can reliably be performed, considering the specific sequence profiles. In this study the applicability of Sequenase for HLA-DPB1 SBT was tested. A panel of samples were typed by SBT at five test sites which participate in the Sequencing Based Typing component of the 12th International Histocompatibility Workshop. The panel represents the existing polymorphism at all known polymorphic positions of exon 2, both in homozygous and heterozygous combinations. The assignment of homozygosity and heterozygosity was validated by Multi-Sequence Analysis, performing cluster analysis of chromatographic data of all sequences at each position. Sequence characteristics were examined and considered for appropriate assignment. Data reveals that Sequenase sequencing can also reliably be used for HLA-DPB1 typing.
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Affiliation(s)
- E H Rozemuller
- Department of Pathology, University Hospital Utrecht, The Netherlands
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21
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Yasunaga S, Kimura A, Hamaguchi K, Ronningen KS, Sasazuki T. Different contribution of HLA-DR and -DQ genes in susceptibility and resistance to insulin-dependent diabetes mellitus (IDDM). TISSUE ANTIGENS 1996; 47:37-48. [PMID: 8929711 DOI: 10.1111/j.1399-0039.1996.tb02512.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Previous studies have indicated that certain alleles of HLA-DR and -DQ genes were strongly associated with susceptibility and resistance to insulin-dependent diabetes mellitus (IDDM), and the role of DQ molecule in IDDM has been suggested. To further clarify the association of DQ alleles with IDDM, we determined the nucleotide sequences of full-length cDNA from 13 DQA1 alleles and 14 DQB1 alleles. The sequencing analysis revealed sequence polymorphisms outside the hypervariable region of DQ genes. We then analyzed the DQA1 and DQB1 polymorphisms along with that of DRB genes in 86 B-lymphoblastoid cell lines (B-LCLs) from various ethnic groups and in healthy unrelated Japanese and Norwegian individuals. The allelic and haplotypic distributions in each population revealed the characteristic haplotypic formation in the HLA class II region. HLA genes in 139 Japanese and 100 Norwegian IDDM patients were analyzed. DQB1*0301 was negatively associated with IDDM in both ethnic groups, irrespective of associated DRB1 and DQA1 alleles. In DQB1*0302 positive populations, which represented a positive association with IDDM in both ethnic groups, DRB1*0401, *0404, *0802 haplotypes increased in the patients, whereas DRB1*0406 haplotype decreased. Considering about the hierarchy in DRB1 alleles with IDDM susceptibility (DRB1*0401>*0404>*0403 in Norwegian and DRB1*0802>*0403>*0406 in Japanese), the genetic predisposition to IDDM is suggested to be defined by the combination of DR-associated susceptibility and DQ-associated susceptibility and by the DQ-associated resistance which is a dominant genetic trait.
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Affiliation(s)
- S Yasunaga
- Department of Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka
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22
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23
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Versluis LF, Verduyn W, van der Zwan A, Marsh SG, Oudshoorn M, Tilanus MG. A complete exon 2 sequence of the HLA-DPA1*02012 allele. TISSUE ANTIGENS 1995; 46:206-7. [PMID: 8525481 DOI: 10.1111/j.1399-0039.1995.tb03121.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- L F Versluis
- Diagnostic DNA Laboratory, University Hospital Utrecht, The Netherlands
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24
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Epplen C, Buitkamp J, Rumpf H, D'Souza M, Epplen JT. Immunoprinting reveals different genetic bases for (auto)immuno diseases. Electrophoresis 1995; 16:1693-7. [PMID: 8582358 DOI: 10.1002/elps.11501601281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The genetic basis of complex (auto)immune diseases has been studied for an ovine nematode infection, human rheumatoid arthritis (RA), early onset pauciarticular arthritis (EOPA) and multiple sclerosis (MS). Immunoprinting combines the powerful simplicity of polymerase chain reaction (PCR)-based amplification of discrete, highly informative microsatellite loci with the principle of genetic associations. This approach has allowed us to define novel genetic risk factors in adult RA patient categories whereas EOPA forms in juveniles display other prominent genetic contributions. Differentially regulated tumor necrosis factor (TNF) expression may lead to a better understanding of the causal pathogenesis of EOPA while T cell receptor (TCR) gene polymorphisms appear crucial for RA manifestations in certain patient groups. Statistically significant marker associations have still to be defined for MS in larger panels of patient and control cohorts. The clinical course of the disease will probably have to be taken into account when associations with lymphokine levels are evaluated. In essence a convoluted myriad of negative and a few positive disease association data have been generated efficiently by immunoprinting. As expected, the interrelationships are truly complicated between the polymorphic genetic instances predisposing to autoimmune disease. Nevertheless, risk factors may be defined on an individualized basis by indirect gene diagnosis revealing predispositions and providing a more solid basis for differential diagnosis and treatment.
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Affiliation(s)
- C Epplen
- Ruhr-Universität, Bochum, Germany
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25
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Rozemuller EH, Eliaou JF, Baxter-Lowe LA, Charron D, Kronick M, Tilanus MG. An evaluation of a multicenter study on HLA-DPB1 typing using solid-phase Taq-cycle sequencing chemistry. TISSUE ANTIGENS 1995; 46:96-103. [PMID: 7482513 DOI: 10.1111/j.1399-0039.1995.tb02484.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In HLA Class II genes, polymorphism is mainly located in the second exon. Most DNA based typing methods are confined to the identification of specific sequence motifs in the second exon. In contrast, Sequencing Based Typing (SBT) elucidates the entire exon 2 sequence for typing. Comparison of the obtained exon 2 sequence with an allele sequence library results in allele assignment. We tested the applicability of SBT using a protocol for amplification followed by solid phase Taq-cycle sequencing for HLA-DPB1 typing. A panel of 32 samples were typed by SBT at five test sites which are participating in the Sequencing Based Typing component of the 12th International Histocompatibility Workshop. The panel represents the existing polymorphism at all known polymorphic positions of exon 2, both in homozygous and heterozygous combinations. In this multicenter study we focused on the reliability of analyzing heterozygous sequences for HLA typing. A multi-sequence analysis approach, Polall, was developed to evaluate sequences obtained. The assignment of homozygosity and heterozygosity was validated by cluster analysis of chromatographic data of all sequences. Sequence characteristics were examined and considered for appropriate assignment. Differences in sequence characteristics that occurred between the test sites are considered in detail. The evaluation of data of 5 test sites reveals that Taq-cycle sequencing can reliably be performed for HLA-DPB1 SBT.
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Affiliation(s)
- E H Rozemuller
- Department of Pathology, University Hospital Utrecht, The Netherlands
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26
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Schwaiger FW, Gostomski D, Stear MJ, Duncan JL, McKellar QA, Epplen JT, Buitkamp J. An ovine major histocompatibility complex DRB1 allele is associated with low faecal egg counts following natural, predominantly Ostertagia circumcincta infection. Int J Parasitol 1995; 25:815-22. [PMID: 7558567 DOI: 10.1016/0020-7519(94)00216-b] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Infection with Ostertagia circumcincta is a major constraint on sheep production in temperate areas of the world. A potential control strategy is the use of genetically resistant sheep. Therefore we examined the association between MHC-DRB1 alleles and faecal egg counts following natural, predominately O. circumcincta infection in a flock of Scottish Blackface sheep. Nineteen DRB1 alleles were identified by a combination of variation in the length of simple repetitive sequences within the intron between exons 2 and 3 and hybridisation of selected oligonucleotides to polymorphisms within exon 2. Faecal samples were taken from 200 lambs from one to six months of age at intervals of 4 weeks. Genetic effects were strongest at 6 months of age. Least-squares analysis indicated that substitution of the most common allele (I) by allele G2 would result in a 58-fold reduction in faecal egg counts in 6-month-old lambs and a 22-fold reduction in 5-month-old lambs. These results suggest that the major histocompatibility complex plays an important role in the development of resistance to O. circumcincta.
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Affiliation(s)
- F W Schwaiger
- Institute for Genetics, Ruhr-Universität, Bochum, Germany
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27
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Arroyo J, Alvarez AM, Nombela C, Sánchez-Pérez M. The role of HLA-DP beta residue 69 in the definition of antibody-binding epitopes. Hum Immunol 1995; 43:219-26. [PMID: 7558939 DOI: 10.1016/0198-8859(95)00022-v] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Residue 69 of the DP beta chain has been previously identified as being involved in T-cell recognition as well as in the susceptibility to certain autoimmune diseases. The codon for Glu 69 in the DPB1*02012 allele was changed to the codon for Lys found in DPB1*0402, and transfectant L cells expressing wild-type or mutant HLA-DP molecule were obtained. The binding of a large panel of mAbs to these transfectants was tested by flow cytometry. Glu to Lys 69 substitution decreased the binding to the DPB1*02012 allele of some of the DP mAbs and completely eliminated the binding of four of the antibodies tested. These results clearly showed that this residue is involved in the formation of DP antibody-binding epitopes. Because this residue should be located in the alpha-helix of the DP beta polypeptide with the side chain pointing into the peptide-binding groove, its implication in the definition in some DP antibody-binding epitopes should be (a) defining conformational epitopes through effects on the conformation of adjacent regions of the molecule, and (b) determining the binding of peptides to the DP cleft which is directly or indirectly involved in these epitopes.
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Affiliation(s)
- J Arroyo
- Department of Microbiology, College of Pharmacy, University Complutense, Madrid, Spain
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28
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Epplen JT, Buitkamp J, Bocker T, Epplen C. Indirect gene diagnoses for complex (multifactorial) diseases--a review. Gene 1995; 159:49-55. [PMID: 7607572 DOI: 10.1016/0378-1119(94)00535-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The analysis of multifactorial diseases requires the efficient investigation of large numbers of (gene) loci and patient (family) samples. Since simple repetitive DNA markers are dispersed all over the chromosomes, molecular techniques employing these tools render most conventional screening procedures obsolete. Examples of tumors, autoimmune diseases and infections are presented to validate concepts of indirect gene diagnoses via simple, tandemly arranged, repetitive DNA sequences. The salient advantages of microsatellite technologies vs. those of multilocus DNA fingerprinting are weighed.
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29
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Epplen JT, Buitkamp J, Epplen C, Mäueler W, Riess O. Indirect DNA/gene diagnoses via electrophoresis--an obsolete principle? Electrophoresis 1995; 16:683-90. [PMID: 7588545 DOI: 10.1002/elps.11501601111] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In principle, gene defects can be investigated directly or indirectly via informative polymorphisms in their vicinity. But because many defects are not yet defined molecularly, these inherited diseases can only be diagnosed indirectly via analysis of informative family situations. Since (multiple) mutation analyses, e.g. via DNA sequencing, are time-consuming and expensive, indirect analysis may still be performed initially--particularly in diseases caused by heterogenous mutations. We focus on diagnoses of neurological and (auto)immune diseases by polymerase chain reaction and separation of the DNA fragments via gel electrophoreses. Even after gene defects have been identified, indirect analysis might be necessary, for example in Huntington's chorea. Although this genetic defect has been characterized as a trinucleotide disease, indirect DNA diagnosis is still performed in particular cases for psychological reasons. The causes of autoimmune diseases are multifactorial and the inheritance is complex, involving several genes. Genome-wide screening programs may involve indirect approaches via analyses of polymorphic microsatellites. Large parts of the immunological genome can be covered when 20 or more genes are investigated simultaneously. Thus the genetic bases of autoimmune diseases are disclosed. Microsatellites themselves could have a biological meaning. We therefore discuss also DNA/protein interactions for simple tandem repeats, the major targets for indirect gene diagnoses. Only indirect evidence exists that certain simple repeats influence genomic (in)stability. Taken together, indirect gene diagnoses supplement direct approaches in a variety of different purposes and in combination with standard electrophoresis techniques.
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30
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Lekutis C, Letvin NL. Biochemical and molecular characterization of rhesus monkey major histocompatibility complex class II DR. Hum Immunol 1995; 43:72-80. [PMID: 7558932 DOI: 10.1016/0198-8859(94)00155-j] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Rapid, simple techniques for MHC class II typing were explored to facilitate the use of a wide variety of nonhuman primate species as models of human diseases and therapies. We demonstrate that radioimmunoprecipitation and 1-D IEF or 1-D NEPHGE can be employed for characterizing MHC class II DR alleles in rhesus monkeys. Complementary molecular analyses have yielded the first full-length nonhuman primate DRA sequence and the first full-length rhesus macaque DRB sequences. In this way it has also been possible to determine which subset of the DRB sequences amplified from a B-LCL are actually expressed.
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Affiliation(s)
- C Lekutis
- Harvard Medical School, New England Regional Primate Research Center, Southborough, Massachusetts, USA
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31
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Zimmerman PA, Phadke PM, Lee A, Elson LH, Aruajo E, Guderian R, Nutman TB. Migration of a novel DQA1* allele (DQA1*0502) from African origin to North and South America. Hum Immunol 1995; 42:233-40. [PMID: 7759311 DOI: 10.1016/0198-8859(94)00107-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A PCR-based strategy termed DHDA has recently been developed which reveals DQA1 and DQB1 allelic polymorphism through gel retardation following electrophoresis. This HLA-typing strategy improves the efficiency of identifying previously undetected DNA sequence polymorphisms. DHDA has been utilized to perform DQA1 genotypic analysis in non-Caucasian populations and has resulted in the identification of a novel allele, DQA1*0502 (designated by the WHO nomenclature committee). This new allele has been found in Africans and South and North Americans of black racial ancestry and is geographically consistent with the African diaspora during the 15th-19th centuries. DQA1*0502 represents a single C-to-G transversion in codon 59 (exon 2) and results in an amino acid change from proline to arginine. Although MHC genes are highly polymorphic, this DQA1*0502 substitution is unique, as it represents an amino acid change at a position assessed previously to be conserved in the human DQ alpha polypeptides.
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Affiliation(s)
- P A Zimmerman
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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32
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Bontrop RE, Otting N, Slierendregt BL, Lanchbury JS. Evolution of major histocompatibility complex polymorphisms and T-cell receptor diversity in primates. Immunol Rev 1995; 143:33-62. [PMID: 7558081 DOI: 10.1111/j.1600-065x.1995.tb00669.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- R E Bontrop
- Biomedical Primate Research Centre-TNO, Rijswijk, The Netherlands
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33
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Rozemuller EH, Bouwens AG, van Oort E, Versluis LF, Marsh SG, Bodmer JG, Tilanus MG. Sequencing-based typing reveals new insight in HLA-DPA1 polymorphism. TISSUE ANTIGENS 1995; 45:57-62. [PMID: 7725312 DOI: 10.1111/j.1399-0039.1995.tb02415.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
An HLA-DPA1 sequencing-based typing (SBT) system has been developed to identify DPA1 alleles. Up to now eight DPA1 alleles have been defined. Six can be discriminated based upon exon 2 polymorphism. The three subtypes of DPA1*01: DPA1*0101, DPA1*0102 and DPA1*0103, have identical exon 2 sequences but show differences in exon 4. Exon 4 sequences were known for only the three DPA1*01 subtypes and for DPA1*0201. We now present additional sequence information for exon 4 and the unknown segments at the 3' end of exon 2. Additionally with the use of this sequencing technique it is also possible to identify previously unidentified polymorphism. We have studied the exon 2 and exon 4 polymorphism of DPA1 in 40 samples which include all known DPA1 alleles. A new allele, DPA1*01 new, was identified which differs by one nucleotide in exon 2 from DPA1*0103, resulting in an aspartic acid at codon 28. The DPA1*01 subtypes DPA1*0101 and DPA1*0102 could not be confirmed in samples which previously were used to define these subtypes, and consequently they do not exist. The exon 4 sequence of DPA1*0201 is corrected based on sequence data of DAUDI, the cell line in which DPA1*0202 was originally defined. The exon 4 regions of the remaining four alleles were resolved: the exon 4 regions of the alleles DPA1*02021 and DPA1*02022 were found to be identical to the--corrected--DPA1*0201 whereas the exon 4 region of DPA1*0301 differs by one nucleotide compared to DPA1*0103. The DPA1*0401 exon 4 region differs by one nucleotide compared to the corrected DPA1*0201.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- E H Rozemuller
- Diagnostic DNA Laboratory, University Hospital Utrecht, The Netherlands
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Han R, Breitburd F, Marche PN, Orth G. Analysis of the nucleotide sequence variation of the antigen-binding domain of DR alpha and DQ alpha molecules as related to the evolution of papillomavirus-induced warts in rabbits. J Invest Dermatol 1994; 103:376-80. [PMID: 7915746 DOI: 10.1111/1523-1747.ep12395285] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We previously found that regression of skin warts induced by the Shope cottontail rabbit papillomavirus in New Zealand White rabbits, as well as malignant conversion of persistent warts, are linked to a restriction fragment length polymorphism of the major histocompatibility complex class II DR alpha and DQ alpha genes. To find out whether this immunogenetic control could be connected with the antigen binding and presentation function of the alpha 1 domain of class II molecules, we have sequenced the exon 2 of the four DR alpha EcoRI and six of the seven DQ alpha PvuII restriction fragment length polymorphism alleles identified, and deduced the encoded amino acid sequences. We found no amino acid polymorphism among DR alpha alleles, indicating that the alpha 1 domain of the DR alpha chain does not condition wart regression or cancer development. In contrast, 27 of the 82 amino acids of the DQ alpha 1 domain were found variable, defining five amino acid sequence alleles. The restriction fragment length polymorphism allele linked to regression and another allele not linked to regression share the same alpha 1 domain, indicating that wart regression is rather conditioned by a closely linked gene. The most divergent DQ alpha 1 allele, however, was that associated with a higher risk of cancer. Alignment of rabbit and human DQ alpha exon 2 alleles disclosed that amino acid charge variations occur at positions assumed to be important for peptide binding in humans. By modulating the affinity for tumor-specific antigenic peptides, such transitions could affect immune surveillance and, thus, condition the risk for progression to carcinoma of papillomavirus-associated lesions.
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Affiliation(s)
- R Han
- Unité des Papillomavirus, INSERM U.190, Paris, France
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35
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Satta Y, O'hUigin C, Takahata N, Klein J. Intensity of natural selection at the major histocompatibility complex loci. Proc Natl Acad Sci U S A 1994; 91:7184-8. [PMID: 8041766 PMCID: PMC44363 DOI: 10.1073/pnas.91.15.7184] [Citation(s) in RCA: 132] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Long persistence of allelic lineages, prevalence of nonsynonymous over synonymous substitutions in the peptide-binding region (PBR), and deviation from neutrality of the expected gene identity parameter F all indicate indirectly that balancing selection is operating at functional major histocompatibility complex (MHC) loci. Direct demonstrations of the existence of balancing selection at MHC loci are, however, either lacking or not fully convincing. To define the conditions under which balancing selection could be demonstrated, we estimated its intensity from the mean number of nonsynonymous substitutions, KB, at the PBR and the mutation rate mu. We compared the five available methods for estimating KB by computer simulation and chose the most reliable ones for estimation of selection intensity. For the human MHC, the selection coefficients of the HLA-A, -B, -C, -DRB1, -DQB1, -DQA1, and -DPB1 loci are 0.015, 0.042, 0.0026, 0.019, 0.0085, 0.0028, and 0.0007, respectively. This low selection intensity places severe restrictions on the possibility of measuring selection directly in vertebrate populations.
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Affiliation(s)
- Y Satta
- Abteilung Immungenetik, Max-Planck-Institut für Biologie, Tübingen, Germany
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36
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Ayala FJ, Escalante A, O'Huigin C, Klein J. Molecular genetics of speciation and human origins. Proc Natl Acad Sci U S A 1994; 91:6787-94. [PMID: 8041698 PMCID: PMC44284 DOI: 10.1073/pnas.91.15.6787] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The major histocompatibility complex (MHC) plays a cardinal role in the defense of vertebrates against parasites and other pathogens. In some genes there are extensive and ancient polymorphisms that have passed from ancestral to descendant species and are shared among contemporary species. The polymorphism at the DRB1 locus, represented by 58 known alleles in humans, has existed for at least 30 million years and is shared by humans, apes, and other primates. The coalescence theory of populations genetics leads to the conclusion that the DRB1 polymorphism requires that the population ancestral to modern humans has maintained a mean effective size of 100,000 individuals over the 30-million-year persistence of this polymorphism. We explore the possibility of occasional population bottlenecks and conclude that the ancestral population could not have at any time consisted of fewer than several thousand individuals. The MHC polymorphisms exclude the theory claiming, on the basis of mitochondrial DNA polymorphisms, that a constriction down to one or few women occurred in Africa, at the transition from archaic to anatomically modern humans, some 200,000 years ago. The data are consistent with, but do not provide specific support for, the claim that human populations throughout the World were at that time replaced by populations migrating from Africa. The MHC and other molecular polymorphisms are consistent with a "multiregional" theory of Pleistocene human evolution that proposes regional continuity of human populations since the time of migrations of Homo erectus to the present, with distinctive regional selective pressures and occasional migrations between populations.
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Affiliation(s)
- F J Ayala
- Department of Ecology and Evolutionary Biology, University of California, Irvine 92717
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Tosi G, Brunelli S, Mantero G, Magalini AR, Soffiati M, Pinelli L, Tridente G, Accolla RS. The complex interplay of the DQB1 and DQA1 loci in the generation of the susceptible and protective phenotype for insulin-dependent diabetes mellitus. Mol Immunol 1994; 31:429-37. [PMID: 8183282 DOI: 10.1016/0161-5890(94)90062-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
IDDM patients of North East Italian region were molecularly typed for their HLA-DQB1 and DQA1 loci by using allele specific oligonucleotide probes and PCR amplified genomic DNA. IDDM status strongly correlated with DQB1 alleles carrying a non-aspartic acid residue in position 57 of DQ beta chain and DQA1 alleles with an arginine residue in position 52 of DQ alpha chain. Genotype analysis revealed that individuals with two DQB1 alleles having a non-aspartic residue in position 57 and two DQA1 alleles with an arginine residue in position 52 had the highest relative risk of disease: they constituted 41% of IDDM patients as compared to 0% of controls. Heterozygosity either at residue 57 of DQB1 or residue 52 of DQA1 was sufficient to abrogate statistical significance for disease association, although 43.6% of IDDM patients were included in these two groups as compared to 21.6% of normal controls. On the other hand the presence of two DQB1 alleles with aspartic acid in position 57 was sufficient to confer resistance to disease irrespective of the DQA1 genotype. Based on the number of possible susceptible heterodimers an individual can form, it was found that 85% of IDDM cases could form two or more heterodimers (two in cis and two in trans), but no IDDM case was found to form one susceptible heterodimer in cis. These results demonstrate that the complete HLA-DQ genotype, more than single DQB1 or DQA1 alleles or DQB1-DQA1 haplotypes, is associated with the highest risk of disease. Screening of the population for preventive purposes and/or early signs of IDDM should then take advantage of this result and "susceptible homozygous" individuals should be followed very closely and considered the first group of choice for possible new therapeutical trials.
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Affiliation(s)
- G Tosi
- Istituto di Immunologia e Malattie Infettive, Facoltà di Medicina e Chirurgia, Università di Verona, Italy
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Laforet M, Urlacher A, Tongio MM. A new HLA DR16 allele (DRB1*1604) with a short DR8 sequence. TISSUE ANTIGENS 1994; 43:257-60. [PMID: 8085262 DOI: 10.1111/j.1399-0039.1994.tb02335.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M Laforet
- Centre Régional de Transfusion Sanguine, Strasbourg, France
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Hashimoto M, Kaneshige T, Kinoshita T, Murayama A, Asai S, Yamasaki M, Nojima M, Ichikawa Y, Fukunishi T. A new DR14-related DRB1 allele, DRB1*1412, which differs from DRB1*1403 only at codon 86. TISSUE ANTIGENS 1994; 43:133-5. [PMID: 8016842 DOI: 10.1111/j.1399-0039.1994.tb02314.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M Hashimoto
- Kidney Transplantation Center, Hyogo Prefectural Nishinomiya Hospital, Japan
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Gläser R, Eiermann TH, Fricke L, Kirchner H, Bein G. HLA DNA preorgan retrieval donor typing in renal transplantation. Vox Sang 1993; 65:300-2. [PMID: 8310682 DOI: 10.1111/j.1423-0410.1993.tb02170.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
For the first time, a DNA technique was used in clinical practice for pre-organ donor retrieval typing in renal transplantation. The method is based on the polymerase chain reaction with nested sequence-specific pairs (nested PCR-SSP) for all serological HLA-DR specificities of DR1-DR18. A panel of reference-typed individuals (n = 101) was investigated in a blind quality control study and the results revealed a sensitivity of 99.5% and a specificity of 100%. Semi-automation of PCR-SSP provided rapid, accurate and reliable typing results demonstrating that this DNA test is most suitable for replacing the error-prone HLA-DR serological technique. Twenty-seven consecutive cadaveric organ donors have been successfully typed so far. The results were available within less than 3 h after blood sampling and in all cases prior to the retrieval of organs. In conclusion, the introduction of this accurate DNA typing in HLA matching programs may significantly improve the graft survival rate in renal transplantation.
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Affiliation(s)
- R Gläser
- Institute of Immunology and Transfusion Medicine, University of Lübeck Medical School, FRG
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Zhang S, Fernandez-Vina M, Falco M, Cerná M, Raimondi E, Stastny P. A novel HLA-DRB1 allele (DRB1*0417) in South American Indians. Immunogenetics 1993; 38:463. [PMID: 8406622 DOI: 10.1007/bf00184531] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S Zhang
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas 75235-8886
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Trtková K, Kupfermann H, Grahovac B, Mayer WE, O'hUigin C, Tichy H, Bontrop R, Klein J. Mhc-DRB genes of platyrrhine primates. Immunogenetics 1993; 38:210-22. [PMID: 8505064 DOI: 10.1007/bf00211521] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The two infraorders of anthropoid primates, Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys and the hominoids) are estimated to have diverged from a common ancestor 37 million years ago. The major histocompatibility complex class II DRB gene and haplotype polymorphism of the Catarrhini has been characterized in several recent studies. The present study was undertaken to obtain information on the DRB polymorphism of the Platyrrhini. Fifty-five complete exon 2 DRB sequences were obtained from six species of Platyrrhini representing both the Callitrichidae and the Cebidae families. Combined with the results of a parallel contig mapping study, our data indicate that at least three loci (DRB1*03, DRB3, and DRB5) are shared by the Catarrhini and the Platyrrhini. However, the three loci are occupied by functional genes in the former infraorder and mostly by pseudogenes in the latter. Instead of the pseudogenes, the Platyrrhini have evolved a new set of apparently functional genes-DRB11 and DRB*W12 through DRB*W19, which have thus far not been found in the Catarrhini. The DRB*W13, *W14, *W15, *W17, *W18, and *W19 genes seem to be restricted to the Cebidae family, whereas the DRB*W16 locus has so far been documented in the Callitrichidae family only. The DRB alleles of the cotton-top tamarin, and perhaps also those of the common marmoset (both members of the family Callitrichidae), are characterized by low nucleotide diversity, possibly indicating that they diverged from a common ancestral gene relatively recently.
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Affiliation(s)
- K Trtková
- Max-Planck-Institut für Biologie, Abteilung Immungenetik, Tübingen, Germany
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Wang Y, Lu P, Zhou K, Clay T, Wood N, Bradley B, Bidwell J. Nucleotide sequencing of HLA-DQ gene second exons in Chinese homozygous cells. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 1992; 19:287-93. [PMID: 1420115 DOI: 10.1111/j.1744-313x.1992.tb00071.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Six HLA class I and class II-homozygous Chinese cell lines with unique HLA-Dw types were studied. Since the majority of HLA class II nucleotide sequence polymorphism is localized within the second exons of the genes, we used the polymerase chain reaction (PCR) to amplify these regions in HLA-DQA and DQB genes and subsequently determined the nucleotide sequences. No unique DQA1 or DQB1 alleles were found. However, a new haplotype of DQA1*0601-DQB1*0301-DRB1*1202 was found in two cells; and DQA1*03011 was found in association with DR9 in another two cells. This indicates that new DR-DQ associations may explain the observed new HLA-Dw types. The DQB2 sequences were identical in all six cells and were identical to a sequence previously reported in a DR6 haplotype. The DQA2 sequences from two clones obtained from two cells differed from each other and from previously reported sequences. The results show that the DQA1 and DQB1 alleles in the Chinese individuals studied are as previously reported in Caucasian populations and as such may be typed by restriction fragment-length polymorphism (RFLP) or PCR-sequence-specific oligonucleotide typing (PCR-SSO) or PCR-RFLP using conventional probe or restriction enzyme sets.
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Affiliation(s)
- Y Wang
- Molecular Genetics Laboratory, United Kingdom Transplant Support Service, Bristol
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