Six HLA-D region alpha-chain genes on human chromosome 6: polymorphisms and associations of DC alpha-related sequences with DR types.

Abstract

The HLA-D region (class II) genes determine cell-surface glycoproteins, which function in the immune response. The known products of these genes are heterodimers of an a and a /3 chain. There are at least three major sets of products coded for by the HLA-D region. These are HLA-DR (homologous to I-E of the mouse H-2 region), defined by conventional serological methods; DC or MT (homologous to mouse I-A), originally defined by the cross-reacting group that included DR1, -2, and -w6; and SB, the "secondary B" cell types defined by primed lymphocyte typing (for reviews, see refs. 1 and 2). A fourth product, closely related to DR and called BR, has also been proposed on the basis of immunochemical analysis (3). Unlike the HLA-A and -B loci, whose original antigens were rapidly "split" to yield more than 20 HLA-A and more than 40 HLA-B alleles, the list of HLA-DR alleles has not yet been greatly expanded. Studies by two-dimensional gel electrophoresis have shown that most of the serologically detected polymorphic variation is attributable to variation in the 83 chains of the DR and DC molecules (1, 4), and DNA probes for the ,B chains have revealed a high level of restriction fragment polymorphism (5, 6). In contrast, probes for the DRa-and SBa-chain genes detect little restriction-site polymorphism among unrelated individuals, while a probe for the DCa chain detects a high level of polymorphism (7,8). These results are consistent with the finding of sequence variation in regions of cDNA clones for DCa and the homologous I-A a chains in mouse (9, 10). In preliminary studies, the variation detected by the DCa probe appeared to be associated with certain patterns of allelic variation in HLA-DR (7,8). The other three class II a-chain genes described previously showed little restriction enzyme polymorphism (7,11).In this paper we describe two additional class II a-chain gene sequences, both on chromosome 6. We have also studied systematically the variation in restriction patterns in two genes as revealed by the DCa-chain probe. Using a panel of cell lines, that are for the most part homozygous for HLA-DR, there is a strong association, due to linkage disequilibrium, between the restriction patterns and the HLA-DR types. Within some DR types, even those that are serologically homogeneous, there is additional polymorphic variation detected at the DNA level for both the DCa and the related DXa genes. MATERIALS AND METHODSEnzymes and Other Reagents. Restriction enzymes were purchased from Cambridge Biotechnology Laboratories and New England Biolabs., radiochemicals were from the Radiochemical Centre, and DNA polymerase I was from Boehringer Mannheim.Cell Lines. All DNA samples were extracted from the lymphoblastoid lines shown in Table 2. Most of the cell lines behaved as homozygous typing cells in the mixed lymphocyte reaction, which detects mainly HLA-DR-associated determinants. The human-mouse hybrids used for assigning sequences to chromosome 6 contained a human X/6 translocation chromosome from the cell line G3.32.2 (7,...

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“…DRa is a Pst I cDNA fragment, 0.3-0.5 kb in length [18]. DQc~ is a Pst 1 2.0 kb genomic fragment and also identifies with the DXc~ gene [19]. DQ[~ is a Ava I cDNA fragment of pDR[31, 0.6 kb in length [20].…”

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“…Although the latter two are nearly identical (they differ at only one position in the first domain, the deletion at the NH2 terminus) the DQ7 a subunit differs by 7 and 8 amino acids in the first domain, respectively. While this may represent an earlier divergence of the DQ9 a subunit, it is also possible that some unusual genetic event has occurred during the evolution of the DR7 haplotype.…”

“…scribed; at present seven P3 chain (two DP, two DQ, and three DR) and five a chain (two DP, two DQ, and one DR) gene loci have been identified (4)(5)(6)(7)(8)(9). Although their precise genetic order is not yet known, the DP locus is known to be centromeric to both DQ and DR, which in turn are centromeric to the class I loci, HLA-A, -B, and -C (10).…”

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“…Large-scale DNA sequencing was not yet an option, but the discovery of polymorphisms detected by the use of restriction enzymes and Southern blotting (the RFLPs) began to provide an answer. Using this technique on DNA samples from individuals of known serological types showed striking associations between the RFLP patterns and serological types, which could in many cases be grouped according to which D region α or β genes were involved (61,67). Thus, it became clear that DR α was hardly at all variable, and therefore the DR serological types must be determined by the DR β gene.…”

“…Having a handle to fish out cosmids from genomic libraries carrying sequences related to DR α, especially using less stringent hybridization conditions, soon led to the discovery of several other D region α genes (61,67). Several of these also contained D region β gene sequences, showing the close genomic relationship between the α and β genes.…”