Abstract
Nucleic acid sequences of the second exons of HLA-DRB1, −DRB3/4/5, −DQB1, and −DQA1 genes were determined from 43 homozygous cell lines, representing each of the known class II haplotypes, and from 30 unrelated Caucasian subjects, comprising 60 haplotypes. This systematic sequence analysis was undertaken in order to a) determine the existence of sequence microheterogeneity among cell lines which type as identical by methods other than sequencing; b) determine whether direct sequencing of class II genes will identify the presence of more extensive sequence polymorphism at the population level than that identified with other typing methods; c) accurately determine the molecular composition of the known class II haplotypes; and d) study their evolutionary relatedness by maximum parsimony analysis. The identification of seven previously unidentified haplotypes carrying five new allelic amino acid sequences suggests that sequence microheterogeneity at the population level may be more frequent than previously thought. Maximum parsimony analysis of these haplotypes allowed their evolutionary classification and indicates that the higher mutation rate at DRB1 compared to DQB1 loci in most haplotypic groups is inversed in specific haplotype lineages. Furthermore, the extent and localization of gene conversions and point mutations at class II loci in the evolution of these haplotypes is significantly different at each locus. Identification of additional HLA class II molecular microheterogeneity suggests that direct sequence analysis of class II HLA genes can uncover new allelic sequences in the population and may represent a useful alternative to current typing methodologies to study the effects of sequence allelism in organ transplantation.
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Andersson, G., Larhammar, D., Widmark, E., Servenius, B., Peterson, P. A., and Rask, L.: Class II genes of the human major histocompatibility complex. Origanization and evolutionary relationship of the DRβ genes. J Biol Chem 262: 8748–8758, 1987
Auffray, C. and Strominger, J. L.: Molecular genetics of the human major histocompatibility complex. Adv Hum Genet 15: 197–247, 1985
Bach, F. H.: Class II genes and products: the HLA-D region. Immunol Today 6: 89–94, 1985
Bidwell, J.: DNA RFLP analysis and genotyping of HLA-DR and DQ antigens. Immunol Today 9: 18–23, 1988
Denaro, M., Hammerling, U., Ras, L., and Peterson, P. A.: The E bβ gene may have acted as the donor gene in a gene conversion-like mechanism generating the A b12β mutant. EMBO J 3: 2029–2032, 1984
Felsenstein, J.: Phylogenies from molecular sequences. Inference and reliability. Annu Rev Genet 22: 521–565, 1988
Flomenberg, N.: Functional polymorphisms of HLA class II gene products detected by T-Lymphocyte clones: Summary of the Tenth International Histocompatibility Workshop cellular studies. In B. Dupont (ed.): Immunobiology of HLA, pp 532–550, Springer, New York, 1989
Gorski, J.: The HLA-DRw8 lineage was generated by a deletion in the DRB region followed by first domain diversification. J Immunol 142: 4041–4045, 1989a
Gorski, J.: HLA-DRβ-chain polymorphism. Second domain polymorphism reflects evolutionary relatedness of allele and may explain public serologic epitopes. J Immunol 143: 329–333, 1989b
Gorski, J. and Mach, B.: Polymorphism of human Ia antigens: gene conversion between two DR β loci results in a new HLA-D/DR specificity. Nature 322: 67–70, 1986
Gregersen, P. K., Moriuchi, T., Karr, R. W., Obata, F., Moriuchi, J., Maccari, J., Goldberg, D., Winchester, R. J., and Silver, J.: Polymorphism of HLA-DRβ chains in DR4, −7 and −9 haplotypes: Implications for the mechanisms of allelic variation. Proc Natl Acad Sci USA 83: 9149–9153, 1986a
Gregersen, P. K., Shen, M., Song, Q.-L., Merryman, P., Degar, S., Seki, T., Maccari, J., Goldberg, D., Murphy, H., Schwenzeer, J., Wang, C. Y., Winchester, R. J., Nepom, G. T., and Silver, J. Molecular diversity of HLA-DR4 haplotypes. Proc Natl Acad Sci USA 83: 2642–2646, 1986b
Gregersen, P. K., Goyert, S. M., Song, Q.-L., and Silver, L: Microheterogeneity of HLA-DR4 haplotypes: DNA sequence analysis of LD“KT2” and LD“TAS” haplotypes. Hum Immunol 19: 287–292, 1987
Gregersen, P. K., Kao, H., Nunez-Roldan, A., Hurley, C. K., Karr, R., and Silver, J.: Recombination sites in the HLA class II region are haplotype dependent. J Immunol 141: 1365–1368, 1988
Gustafsson, K., Wiman, K., Emmoth, E., Larhammar, D., Bohme, J., Hyldig-Nielsen, J. J., Ronne, H., Peterson, P. A., and Rask, L.: Mutation and selection in the generation of class II histocompatibility antigen polymorphism. EMBO J 3: 1655–1661, 1984
Gyllensten, U. B. and Erlich, H. A.: Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc Natl Acad Sci USA 85: 7652–7656, 1988
Gyllensten, U. B. and Erlich, H. A.: Ancient roots for polymorphism at the HLA-DQδ locus in primates. Proc Natl Acad Sci USA 86:: 7652–7656, 1988
Horn, G. T., Bugawan, T. L., Long, C. M., and Erlich, H. A.: Allelic sequence variation of the HLA-DQ loci: relationship to serology and to insulindependent diabetes susceptibility. Proc Natl Acad Sci USA 85: 6012–6016, 1988
Hurley, C. K., Ziff, B. L., Silver, J., Gregersen, P. K., Hartzman, R., and Johnson, A.: Polymorphism of the HLA-DR1 haplotype in American blacks. J Immunol 140: 4019–4023, 1988
Kao, H.-T., Gregersen, P. K., Tang, J. C., Takahashi, T., Wang, C. Y., and Silver, J.: Molecular analysis of the HLA class II genes in two DRw6-related haplotypes. DRw13-DQw1 and DRw14-DQw3. J Immunol 142 : 1743–1747, 1989
Knowles, R. W.: Structural polymorphism of the HLA class II α and β chains: Summary of the 10th Workshop 2-D Gel Analysis. In B. Dupont (ed.): Immunobiology of HLA, pp. 365–380, Springer, New York, 1989
Layrisse, Z., Simoney, N., Park, M. S., and Terasaki, P. I.: HLA-D and DRw determinants in an american indigenous isolate. Transplant Proc XI: 1788–1791, 1979
Lee, B. S. M., Bell, J. I., Rust, N. A., and McDevitt, H. O.: Structural and functional variability among DQβ alleles of DR2 subtypes. Immunogenetics 26: 85–91, 1987
Liu, C.-P., Bach, F. H., and Wu, S.: Molecular studies of a rare DR2/LD-5a/DQw3 HLA class II haplotype. Multiple mechanisms in the generation of polymorphic HLA class II genes. J Immunol 140: 3631–3639, 1988
Marsh, S. G. E. and Bodmer, J. G.: HLA-DR and −DQ epitopes and monoclonal atibody specificity. Immunol Today 10: 305–312, 1989
Mattiuz, P. L., Cambon-Thomsen, A., Goeken, N., Kaplan, C., and Calot, M.: Antigen Society number 26 Report (DR3, DR7, DQw2): HLA-DQw2. In B. Dupont et al. (eds.): Immunobiology of HLA, pp. 263–266, Springer, New York, 1989
Mengle-Law, L., Conner, S., McDevitt, H. O., and Fathman, C. G.: Gene conversion between murine class II major histocompatibility complex loci. Functional and molecular evidence from the bm12 mutant. J Exp Med 160: 1184–1194, 1984
Merryman, P., Gregersen, P. K., Lee, S., Silver, J., Nunez-Roldan, A., Crapper, R., and Winchester, R.: Nucleotide sequence of a DRw10 β chain cDNA clone. Identity of the third D region with that of the DRw53 allele of the β2 locus and as the probable site encoding a polymorphic MHC class II epitope. J Immunol 140: 2447–2452, 1988
Merryman, P., Silver, J., Gregersen, P. K., Solomon, G., and Winchester, R.: A novel association of DQA and DQB genes in the DRw10 haplotype. Determination of a DQw1 specificity by the DQβ chain. J Immunol 143: 2068–2073, 1989
Noreen, H. J., Santamaria, P., Davidson, M. L., Rich, S. S., and Segall, M.: Serology, RFLP and sequence analysis of a unique HLA class II antigen, DR5x6. Hum Immunol 30: 168–173, 1991
Rask, L. K., Gustafsson, K., Larhammer, D., Ronne, H., and Peterson, P. A.: Generation of class II antigen polymorphism. Immunol Rev 84: 123–143, 1985
Tieber, V., Abruzzini, L., Didier, D. K., Schwartz, B., and Rotwein, P.: Complete characterization and sequence of an HLA class II DRβ chain cDNA from the DR5 haplotype. J Biol Chem 261: 2738–2742, 1986
Tiercy, J. M., Gorski, J., Jeannet, M., and Mach, B.: Identification and distribution of three serologically undetected alleles of HLA-DR by oligonucleote DNA typing analysis. Proc Natl Acad Sci USA 85: 198–202, 1988
Todd, J. A., Bell, J. I., and McDevitt, H. O.: HLA-DQB gene contributes to susceptibility and resistance to insulin-dependent diabetes mellitus. Nature 329: 599–604, 1987
Widera, G. and Flavell, R. A.: The nucleotide sequence of the murine I-E bβ immune response gene: evidence for gene conversion events in class II genes of the major histocompatibility complex. EMBO J 3: 1221–1225, 1984
WHO Nomenclature Committee: Nomenclature for factors of the HLA system, 1989. Immunogenetics 31: 131–140, 1990
Wu, S., Sauders, T. L., and Bach, F. H.: Polymorphism of human Ia antigens generated by reciprocal intergenic exchange between two DRB loci. Nature 324: 676–679, 1986
Young, J. A. T., Wilkinson, D., Bodmer, W. F., and Trowsdale, J.: Sequence and evolution of HLA-DR7 and –DRw53-associated β chain genes. Proc Natl Acad Sci USA 84: 4929–4933, 1987
Zinkernagel, R. M. and Doherty, P. C.: Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system Nature 248: 701–703, 1974
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The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M35890 through M35953.
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Santamaria, P., Boyce-Jacino, M.T., Lindstrom, A.L. et al. Detection of novel sequence heterogeneity and haplotypic diversity of HLA class II genes. Immunogenetics 33, 374–387 (1991). https://doi.org/10.1007/BF00216697
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DOI: https://doi.org/10.1007/BF00216697