Genes of the major histocompatibility complex in mouse and man

Cloning and sequence analysis of the human major histocompatibility complex gene DC-3 beta

The DC antigen is one of the class II major histocompatibility antigens involved in the regulation of the immune response. This molecule is a heterodimer composed of an alpha and a beta chain. Southern blot analysis of several homozygous cell lines shows that there are two DC beta genes. The DC-3 beta gene, corresponding to a polymorphic restriction fragment, was cloned and sequenced and found to exist in five exons spanning 8 kilobase pairs of DNA. These exons correspond to the functional domains of the DC beta protein. Comparison of the beta 1 domains of known DC beta chains shows that the polymorphism is clustered in four regions. A similar comparison of the mouse A beta sequences shows only two prominent diversity regions. The DC beta chain sequences are eight amino acids shorter than the A beta chain sequences due to the elimination of a small exon by an aberrant splice acceptor.

Linkage map of two HLA-SB beta and two HLA-SB alpha-related genes: an intron in one of the SB beta genes contains a processed pseudogene

Three overlapping cosmid clones contain coding sequences for four HLA Class II genes, provisionally identified as two HLA-SB alpha and two HLA-SB beta genes. The genes are in the order beta, alpha, beta, alpha, inverted with respect to each other. One of the SB beta genes contains a 513 bp sequence that appears to be a processed pseudogene, flanked by direct 17 bp repeat sequences, in the intron upstream of the beta 1 exon. The pseudogene is homologous to a family of sequences of approximately 25-40 members, most of which are not on chromosome 6. A cDNA clone, highly homologous to the pseudogene, except for its 5' end, contains a normal poly(A) addition site and a poly(A) tail. The cDNA clone is homologous to a single-copy gene in both man and mouse, encoded on human chromosome 15. A search of published DNA sequences identified a mouse sequence, with about 77% similarity to the pseudogene sequence, in the negative strand of an intron in a mouse dihydrofolate reductase gene. The second SB beta gene does not contain the pseudogene sequence.

Cytolytic T cells recognize the two amino-terminal domains of H-2 K antigens in tandem in influenza A infected cells

We have genetically engineered three alleles of the K locus of the major histocompatibility complex (MHC) of the mouse. These novel hybrid H-2K genes were introduced into mouse 1T 22-6 cells (H-2q), and their products were shown to be expressed on the cell surface. The hybrid H-2 K antigens were examined for their ability to function as restricting elements for cytotoxic T lymphocytes during influenza A infection. Both the alpha 1 and alpha 2 domains of the Kd antigen were required for T cell recognition. This implies an important role for "conformational determinants" on H-2 antigens acting as restricting elements. The cytoplasmic domain of the Kb antigen is not phenotypically important for recognition by T cells.

Class I, II and III major histocompatibility complex gene polymorphisms in BB rats

The BB rat spontaneously develops insulin-dependent diabetes mellitus of autoimmune aetiology. From breeding studies, one of the genes necessary for the development of diabetes in these animals is linked to RT1, the rat's major histocompatibility complex. To study further the RT1 linked diabetogenic gene of the BB rat, we have studied restriction fragment length polymorphism using 32P-labelled DNA probes of the major histocompatibility complex genes. As we have previously reported, an I-A alpha probe (mouse class II gene) defines four chromosome types in the control BBN population, only one of which is found among diabetes prone BB rats. All BB rats we have studied are homozygous for the type IIa chromosome. Here we examine restriction fragment length polymorphisms using three other DNA probes. Using a DC beta-probe (human class II), the same pattern of polymorphisms (though different molecular weights) is found as with the I-A alpha probe. An H-2d C4 (fourth component of complement, mouse class III) defines no polymorphisms among or between BB and BBN rats. Using H-2 LdC-2 domain probe (mouse class I) many polymorphisms are apparent and in a limited series distinguishes I-A alpha defined IIa/IIa BBN rats from IIa/IIa BB rats. These studies provide the basis to subtype the RT1u identical BB and BBN animals and should aid in the localization and characterization of the RT1 linked diabetogenic gene of the BB rat.

The T cell receptor beta chain genes are located on chromosome 6 in mice and chromosome 7 in humans

Homologous clones that encode the beta chain of the T cell antigen receptor have been isolated recently from both murine and human cDNA libraries. These cDNA clones have been used in connection with interspecies hybrid cell lines to determine that the murine T cell receptor gene is located on chromosome 6 and the human gene on chromosome 7. In situ hybridization confirms these data and further localizes these genes to band B of chromosome 6 in the mouse and bands 7p13-21 in the human genome. The organization of the T cell antigen receptor J beta gene segments and C beta genes appears to be conserved, since very few intraspecies polymorphisms of restriction fragment length have been detected in either mouse or human DNA.

Molecular organization of the HLA-SB region of the human major histocompatibility complex and evidence for two SB beta-chain genes

The class II products of the major histocompatibility complex, also called Ia antigens, are composed of two polypeptide chains, the alpha and beta chains, both encoded within the major histocompatibility complex. In man, the class II antigens can be divided into three biochemically distinct groups called HLA-DR, HLA-DC, and HLA-SB. Our isolation of cDNA clones for the polymorphic beta chain of HLA-DR and HLA-DC has allowed us to study the organization of the class II genes. Here we identify the HLA-SB beta-chain gene in recombinant clones from a cosmid library generated from a consanguineous homozygous B-cell line. The SB beta-chain gene is linked to the SB alpha-chain gene and the two genes are in opposite orientation. A second SB beta-chain gene, corresponding to a new SB beta II locus, has also been identified and cloned. The SB beta-chain genes show much less allelic restriction site polymorphism than the genes for the beta chains of HLA-DR or HLA-DC.

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

Analysis of cosmid clones containing genes related to the HLA-DR alpha chain calls for at least six HLA-D region alpha-chain coding sequences in man; namely, DR alpha, DC alpha, DX alpha (very closely related to DC alpha), SB alpha 1, SB alpha 2 (two closely linked genes on the same cosmid clones), and DZ alpha. The first four genes have been described previously. SB alpha 2 and DZ alpha are recently identified genes, characterized by their unique and, from a limited study, nonpolymorphic bands when used as probes for human DNA on Southern blots. All of the genes are present in somatic cell hybrids containing a human X/6 translocation chromosome, and so they are all presumably in the HLA region. The polymorphisms in the region of the DC alpha and related DX alpha genes were studied with Southern blots of DNA from a set of mostly homozygous HLA-D-typing cell lines. With EcoRI, the band patterns for the DC alpha gene corresponded to the major cross-reactive HLA-DR serotypes associated with DC (namely MT1, -2, and -3) while the DX alpha band was invariant. Both genes were polymorphic with the enzyme Taq I. Within some DR types additional polymorphic variation was detected at the DNA level, implying the existence of subtypes. The pattern of polymorphisms for DC alpha, and to a lesser extent for DX alpha, suggests that these genes may play an important role in certain HLA-D associations with disease.

Complete nucleotide sequence of a gene encoding a functional human class I histocompatibility antigen (HLA-CW3)

The HLA-CW3 gene contained in a cosmid clone identified by transfection expression experiments has been completely sequenced. This provides, for the first time, data on the structure of HLA-C locus products and constitutes, together with that of the gene coding for HLA-A3, the first complete nucleotide sequences of genes coding for serologically defined class I HLA molecules. In contrast to the organisation of the two class I HLA pseudogenes whose sequences have previously been determined, the sequence of the HLA-CW3 gene reveals an additional cytoplasmic encoding domain, making the organisation of this gene very similar to that of known H-2 class I genes and also the HLA-A3 gene. The deduced amino acid sequences of HLA-CW3 and HLA-A3 now allow a systematic comparison of such sequences of HLA class I molecules from the three classical transplantation antigen loci A, B, C. The compared sequences include the previously determined partial amino acid sequences of HLA-B7, HLA-B40, HLA-A2 and HLA-A28. The comparisons confirm the extreme polymorphism of HLA classical class I molecules, and permit a study of the level of diversity and the location of sequence differences. The distribution of differences is not uniform, most of them being located in the first and second extracellular domains, the third extracellular domain is extremely conserved, and the cytoplasmic domain is also a variable region. Although it is difficult to determine locus-specific regions, we have identified several candidate positions which may be C locus-specific.

Functional and inducible expression of a transfected murine class II major histocompatibility complex gene

Using the spheroplast fusion technique, we have introduced the cloned E beta b gene into two d haplotype cell lines, the B lymphoma line A20-2J and the macrophage tumor line P388D1. Analysis with a monoclonal antibody indicates that the product of the transfected E beta b gene associates with the endogenous E alpha chain to form an E alpha dE beta b complex. While expression of E alpha dE beta b is constitutive in A20-2J cells transfected with the E beta b gene, surface expression of E alpha dE beta b is detected in transfected macrophage cells only after treatment of cells with culture supernatants from concanavalin A (Con A)-stimulated T cells. Transfected B lymphoma cells and transfected Con A supernatant-treated macrophage cells have acquired the ability to present antigen to E alpha dE beta b-restricted T-cell hybridomas. The observed inducible expression of the transfected gene in the macrophage host indicates that sequences responsible for regulated expression of the E beta b gene may be associated with the transfected gene. In combination with directed mutagenesis, the system described here provides a means to study (i) E beta b sequences that are important in determining the restriction specificity of the E molecule and (ii) sequences associated with the E beta gene that may be important in the regulation of E beta chain expression.

Complete nucleotide sequence of a functional class I HLA gene, HLA-A3: implications for the evolution of HLA genes

The complete nucleotide sequence of an active class I HLA gene, HLA-A3, has been determined. This sequence, together with that obtained for the HLA-CW3 gene, represents the first complete nucleotide sequence to be determined for functional class I HLA genes. The gene organisation of HLA-A3 closely resembles that of class I H-2 genes in mouse: it shows a signal exon, three exons encoding the three extracellular domains, one exon encoding the transmembrane region and three exons encoding the cytoplasmic domain. The complete nucleotide sequences of the active HLA genes, HLA-A3 and HLA-CW3, now permit a meaningful comparison of the nucleotide sequences of class I HLA genes by alignment with the sequence established for a HLA-B7-specific cDNA clone and the sequences of two HLA class I pseudogenes HLA 12.4 and LN- 11A . The comparisons show that there is a non-random pattern of nucleotide differences in both exonic and intronic regions featuring segmental homologies over short regions, which is indicative of a gene conversion mechanism. In addition, analysis of the frequency of nucleotide substitution at the three base positions within the codons of the functional genes HLA-A3, HLA-B7 and HLA-CW3 shows that the pattern of nucleotide substitution in the exon coding for the 3rd extracellular domain is consistent with strong selection pressure to conserve the sequence. The distribution of nucleotide variation in the other exons specifying the mature protein is nearly random with respect to the frequencies of substitution at the three nucleotide positions of their codons. The evolutionary implications of these findings are discussed.

The MT3 specificity resides on a novel human class II antigen distinct from the HLA-DR antigen and DC-like antigen

The MT3 specificity is closely associated with the HLA-DR4, DR7, and DRw9, and is a supertypic specificity. To determine whether the MT3 specificity resides on a novel class II antigen, the MT3 antigen, DR antigen and the DC-like antigen from the DR4-, DR7- and DRw9-homozygous B lymphoid cell lines were identified and compared with one another by two-dimensional gel electrophoresis using alloantisera. The analysis revealed that each of the three antigens exists as a structurally distinct class II antigen in each cell line. The light chains of the MT3, DR and DC-like antigens are different in charge from one another. The molecular weight of the heavy chains of the MT3 and DR antigens is higher than that of the DC-like antigen. On the other hand, no electrophoretic differences are observed between the heavy chains of the MT3 and DR antigens. These results strongly suggest that the MT3 specificity resides on a light chain of a novel class II antigen distinct from the DR antigen and the DC-like antigen. These observations also support our previous proposition that the MT3 antigen belongs to the fourth group of the human class II antigens.

Immunological surveillance of tumors in the context of major histocompatibility complex restriction of T cell function

The immunological surveillance hypothesis was formulated prior to the realization of the fact that an individual's effector T cells generally only see neoantigen if it is appropriately presented in the context of self MHC glycoproteins. The biological consequence of this mechanism is that T lymphocytes are focused onto modified cell-surface rather than onto free antigen. The discovery of MHC-restricted T cell recognition, and the realization that T cell-mediated immunity is of prime importance in promoting recovery from infectious processes, has thus changed the whole emphasis of the surveillance argument. Though the immunological surveillance hypothesis generated considerable discussion and many good experiments, there is no point in continuing the debate in the intellectual context that seemed reasonable in 1970. It is now much more sensible to think of "natural surveillance" and "T cell surveillance," without excluding the probability that these two systems have elements in common. We can now see that T cell surveillance probably operates well in some situations, but is quite ineffective in many others. Part of the reason for this may be that the host response selects tumor clones that are modified so as to be no longer recognized by cytotoxic T cells. The possibility that this reflects changes in MHC phenotype has been investigated, and found to be the case, for some experimental tumors. In this regard, it is worth remembering that many "mutations" in MHC genes that completely change the spectrum of T cell recognition are serologically silent. The availability of molecular probes for investigating the status of MHC genes in tumor cells, together with the capacity to develop cloned T cell lines, monoclonal antibodies to putative tumor antigens, and cell lines transfected with genes coding for these molecules, indicates how T cell surveillance may profitably be explored further in both experimental and human situations.