The origins of HLA-A,B,C polymorphism

Interactions of HLA-B*4801 with peptide and CD8

Functional properties of the B*4801 allotype were investigated using HLA class I-deficient 221 cells transfected with B*4801 cDNA. From pool sequence analysis of endogenously bound peptides, B*4801 was shown to select for nonamer peptides having glutamine or lysine at position 2 and leucine at the carboxyl-terminus. In an in vitro cell-cell binding assay, B*4801 binds CD8 alpha homodimers weakly due to the presence of a threonine residue at position 245 in the alpha 3 domain. A mutant B*4801 molecule in which alanine replaces threonine 245, binds CD8 alpha homodimers at levels comparable to those of other HLA class I allotypes. Despite the low affinity of B*4801 for CD8 alpha, alloreactive T-cells that recognize B*4801 molecules expressed by the 221 transfectant are inhibited by anti-CD8 monoclonal antibodies. Analysis of 25 B*48-expressing individuals from various populations showed threonine 245 was encoded by every B*48 allele.

Three newly identified A*24 alleles: A*2406, A*2413 and A*2414

Three previously unknown A24-related alleles were identified by PCR-SSO typing and confirmed by DNA sequencing in Australian Aboriginal populations (A*2406, 2413) and in individuals of South American descent (A*2414). A*2406 and A*2413 both have two adjacent (but different) nucleotide substitutions in codon 156 in exon 3 compared to A*2402, resulting in a single amino acid replacement in each allele. The South American A*2414 is apparently a hybrid between A2 and A24 with a segment of the A*24 sequence between codons 95 and 107 in exon 3 replaced with the A*02 sequence. Interallelic sequence exchange is the most likely mechanism in the generation of all three novel alleles. Compared to A*2402, the four amino acid substitutions in the A*2414 molecule would be expected to significantly change the shape of the peptide binding cleft, leading to selection of different peptide ligands. The single amino acid replacements in position 156 of the two Australian Aboriginal A*24 alleles may also have significant functional effects. In particular, Trp replacing Gln in position 156 (A*2406) is predicted to markedly reduce the volume of the peptide binding cleft, influence the interaction of HLA pockets with peptide side chains, and therefore, cause major changes in peptide presentation. These newly defined alleles may reflect the adaptive process of HLA genes to local environments.

A new HLA-B44 variant (B44BO [B*4408]) identified by serology

Using HLA serology, we detected a new variant of HLA-B44- B44BO- in two families. This antigen reacts with B44 antisera and is negative with over one-third of B12 (B44, B45) sera but reacts with 50% antisera with a B62 component, especially if they contain anti-B57. The variant, B*4408, differs from the common B*4402 by 4 nucleotide substitutions in exon 2: 193, 206 and 209, which produce changes in the the alpha 1 domain at positions 41, 45 and 46 (TKE in B*4402 and AMA in B44BO); and nucleotide 213, a silent substitution. At each of these positions, B*4408 is identical to B*46 B*57 and may B*15 alleles. As anticipated from its predicted iso-electric point (5.71), one-dimensional isoelectric focusing studies showed that B44BO focuses at the same position as B*4402. The sequence and serological reactivity of this rare antigen allowed the identification of two likely epitopes shared by two different groups of HLA-B antigens.

Analysis of a sequenced cDNA library from multiple sclerosis lesions

To identify genes that are expressed in MS pathogenesis, we have analyzed a normalized cDNA library made from mRNA obtained from CNS lesions of a patient with primary progressive MS. Complementary DNA clones obtained from this library were subjected to automated DNA sequencing to generate expressed sequence tags. Analysis of this MS cDNA library revealed the presence of 54 cDNAs that were associated with immune activation and indicated the presence of an ongoing inflammatory response with evidence of both cell-mediated and humoral immune responses. The surprising finding was that 16 of the cDNAs encoded autoantigens associated with seven other autoimmune disorders, while only three of these 16 autoantigen cDNAs were present in a similarly constructed adult brain library. Such aberrant autoantigen expression could provide a source of secondary autoimmune stimulation that could contribute to the ongoing inflammatory response in MS. In addition, two cDNAs were found that mapped to a known MS susceptibility locus (5p14-p12): one encoded an excitatory amino acid transporter and the other a human homologue of the Drosophila disabled gene. This approach to the molecular biology of MS pathogenesis may help to illuminate previously unappreciated aspects of this disease.

Interferon-gamma rapidly increases peptide transporter (TAP) subunit expression and peptide transport capacity in endothelial cells

Human cytotoxic T lymphocytes (CTL) recognize specific complexes of HLA class I molecules and peptides, which assemble when nascent class I molecules bind peptides transported from the cytoplasm into the endoplasmic reticulum by the heterodimeric transporter associated with antigen processing (TAP). Increased class I molecule expression on the cell surface increases the efficiency of CTL lysis. The kinetics of interferon (IFN)-gamma induction of TAP, peptide transport capacity, and HLA class I molecule expression was determined in endothelial cells, which are targets of CTL following transplantation or viral infection. TAP mRNAs are induced rapidly, increasing 20-fold (TAP1) or 10-fold (TAP2) by 12 h, whereas HLA class I mRNA is induced more slowly, increasing 10-fold in 24 h. TAP1 and TAP2 proteins are also induced rapidly, increasing 10-fold in 24 h, whereas HLA class I heavy chain proteins and surface expression increase more slowly. Peptide transport capacity in endothelial and HeLa cells increases within 6 h of IFN-gamma treatment, suggesting that the IFN-gamma-induced TAP heterodimers are functional. Therefore, the IFN-gamma-induced increase in TAP proteins is accompanied by an increased peptide transport capacity, which may be important in supporting the subsequent rise in HLA class I protein expression.

Polymorphism at codons 114, 116, 145, and 163 muddle the typing of HLA-B*1304

Genetic exchanges often muddle the typing of HLA class I molecules, this is also the case for HLA-B*1304. Serologic and molecular DNA class I typing report a B15/B55 type for cell 847, whereas DNA sequencing finds B*5501/B*1304. HLA-B*1304 differs by no more than four amino acids from other HLA-B13 molecules, a comparative analysis of the B13 and B15 families was therefore performed to determine why serologic and molecular DNA approaches report a B15 type for B*1304. Comparisons demonstrate that limited differences individuate the B15 and B13 molecules such that the genetic recombination of codons 145 and 163 in the class I heavy chain's alpha 2 alpha helix prompt B*1304 to exhibit a B15X21 pattern of serologic cross-reactivity. Molecular DNA class I typing approaches are also swayed by genetic recombinations to type B*1304 as a B15 molecule: B15-like nucleotide sequences encoding residues 114, 116, and 145, lead B*1304 to exhibit a B15 PCR amplification pattern. Thus, genetic exchanges encoding key amino acids in the class I heavy chain lead molecular and serologic typing approaches to categorize HLA-B*1304 as a member of the B15 family.

HLA-B27 (B*2701) specificity for peptides lacking Arg2 is determined by polymorphism outside the B pocket

B*2701 differs from B*2705-by three amino acid changes: D-->Y74, D-->N77, L-->A81, and from B*2702 only by two: D-->Y74 and T-->I80. Tyr74 is located in the C/F cavity of the peptide-binding site, and is unique to B*2701 among HLA-B27 subtypes. Binding of natural B*2705 and B*2702 ligands to B*2701, and to mutants mimicking subtype changes, was analyzed. In addition, sequencing of the peptides bound in vivo by B*2701 and the Y74 mutant was carried out. The main distinctive feature of B*2701 was its presentation of peptides with Gln2. Synthetic analogs bound in vitro similarly as the corresponding ligands with Arg2. Moreover, both Gln2 and Arg2 were dominant upon pool sequencing of B*2701-bound peptides, and 2 of 8 natural ligands contained Gln2. Suitability of Gln2 was largely determined by the Y74 change, as indicated by: 1) binding of Gln2 analogs to this mutant, and 2) detection of Gln2 by pool sequencing of Y74-bound peptides. B*2701 bound peptides with C-terminal aromatic or Leu residues, and interacted with these motifs more strongly than B*2702. The Y74 mutation alone was not responsible for poor binding of peptides with C-terminal basic residues to B*2701, since they bound efficiently and at least one was presented in vivo by this mutant. Most peptides bound to the A81 mutant worse than to B*2705, but frequently better than to B*2701 or B*2702, suggesting that other subtype changes were compensatory. The peptide specificity of B*2701 suggests that this subtype may determine susceptibility to spondyloarthropathy.

Factors influencing the outcome of bone marrow transplants using unrelated donors

The use of unrelated donors for bone marrow transplantation (BMT) is associated with an increased morbidity and mortality when compared with HLA-identical donors, primarily due to an increased rate of graft-versus-host disease, but also to increased susceptibility to infections and graft failure. HLA matching for donors and recipients is the single most important factor influencing the outcome of BMT. However, unrelated donor selection generally relies on matching only for HLA-A, -B and -DR antigens without considering potential incompatibility for other HLA loci, such as HLA-C, -DQ and -DP. In addition, other factors that affect the outcome of BMT need to be taken into consideration in selecting the best unrelated donor. In this review, we will focus on the effects of HLA-associated factors in determining the result of a transplant procedure. We will also mention other relevant factors, drawing on our experience of laboratory studies performed at The Anthony Nolan Research Institute and clinical studies at the Hammersmith Hospital in London.

Identification of a novel HLA-B allele (B*4202) in a Saudi Arabian family with Behçet's disease

A new HLA-B antigen, tentatively called HLA-B42AND, was identified as a B42 serologic variant in a Saudi Arabian family. DNA sequencing analysis of the second and third exon of this new B allele revealed that B42AND was identical to B*4201 except for a single T to C substitution at position 97 of exon 2. This substitution results in histidine (CAC) at codon 9 in B42AND instead of tyrosine (TAC) in B*4201. The antigen frequency of B42AND in a Saudi Arabian population was around 10%. This novel B42AND has officially been named HLA-B*4202.

Molecular analysis of HLA-B35 alleles and their relationship to HLA-B15 alleles

The HLA-B35 serotype is one of the largest allelic groups of HLA class I molecules and includes four isotypes. Of the four, the B35 variant isoform is relatively rare and is the most acidic form. DNA sequencing of the rare isoforms revealed three alleles, B*1522, B*3511, and B*3517. A phylogenetic tree of HLA-B15- and HLA-B35-related alleles for the exon 2 and 3 nucleotide sequences showed that exon 2 of B*1522 clusters with B35 alleles whereas exon 3 clusters with B15 alleles. Branches of the tree suggest that the serodeterminants of B35, B62, B63, and B70 may reside in the alpha 1 domain, encoded by exon 2. The B*1520 and B*1522 genes, which type as B62 and B35, respectively, are hybrid molecules alternatively using exon 2 and exon 3 sequences of B*3501 and B*1501. A comparison of intron 2 sequences for B*3501, B*1501 and B*1522 suggests that the recombination site may have been in the region at the 3' end of intron 2. Despite being flanked by two highly polymorphic exons (exons 2 and 3), intron 2 is relatively well conserved in the B-locus, and it is characterized by seven to eight tandem repeats of the CGGGG pentanucleotide. A high degree of sequence homology and repetitive sequences are essential for a significant frequency of recombination. In this report, we reveal more about the complex evolutionary history of the HLA-B alleles.

HLA-G gene polymorphism segregation within CEPH reference families

HLA-G, a nonclassical HLA class I antigen, presents tissue-restricted expression on human trophoblasts and may play an important role in immune tolerance of mother-versus-fetus. In this work we have demonstrated extensive HLA-G genomic polymorphism within three CEPH reference families, by PCR-SSCP analysis and direct sequencing. Among six unrelated parents we assigned eight HLA-G alleles, seven of which are new. We observed the segregation of HLA-G alleles of heterozygous parents among their offspring that matched the segregation of the HLA class I haplotypes. Only one of the mutations observed was found to be nonsynonymous indicating low polymorphism of the HLA-G molecule.

High polymorphism of Mhc-E locus in non-human primates: alleles with identical exon 2 and 3 are found in two different species

Thirteen Mhc-E new sequences were found in eight individuals belonging to the Cercopithecinae family, i.e.: Macaca mulatta, Macaca fascicularis and Cercopithecus aethiops when studying E locus polymorphism. No changes were found in the invariant residues which are required for the correct conformation of the peptide presenting region which are conserved in classical Mhc class I molecules from fish and reptiles to humans; however, polymorphism of Mhc-E alleles is not limited to the three typical hypervariable regions per domain as it is in classical class I alleles. The rate of synonymous and nonsynonymous substitutions in the DNA sequence corresponding to the antigen binding site, compared to the remainder of exons 2 and 3 shows that the peptide-binding site is under high evolutionary pressure for stability since only synonymous substitutions have been found to be accepted in apes. Also, a clear example of trans-species evolution of allelism is found: two identical exon 2 and exon 3 sequences there exist belonging to individuals from different species (Mamu-Mhc-E*0101 and Mafa-Mhc-E*04). In addition, two Macaca mulatta individuals show an Mhc-E locus duplication. Finally, phylogenetic tree analysis shows that Mhc class I molecules found in Saguinus oedipus (described as Mhc-G homologues) are closer to Mhc-E sequences.

Killer cell receptors: keeping pace with MHC class I evolution

NK cells express receptors that bind to polymorphic determinants of MHC class I heavy chains. MHC ligands vary greatly between mammalian species, and the use of distinct molecular families of NK cell receptors by humans and mice suggests that the receptors too can be evolving rapidly. The KIR (killer cell inhibitory receptor) family of receptors are found in primates and recognize class I epitopes that are of relatively recent origin in primate evolution. Therefore, KIR molecules have probably evolved class I receptor function more recently than C-type lectins, which are represented in both humans and mice. Individual humans express NK cell receptors for which they have no class I ligand, demonstrating a looseness in the coupling of expression between the receptors and their ligands. However, study of a single donor suggests that every NK cell expresses at least one inhibitory receptor for a self-HLA class I allotype, consistent with the missing self hypothesis. Thus the NK-cell receptor-class I interaction appears to control the NK-cell repertoire during ontogeny of the individual and has the potential to be a selective factor influencing both MHC class I and NK cell receptor diversity in the evolution of populations and species.

HLA-C revisited. Ten years of change

During the past 10 years knowledge about the interactions between major histocompatibility complex (MHC) class I molecules and the T-cell receptor (TCR) complex of cytotoxic T-cells (CTL) has developed dramatically. But the primary interest, both with respect to structure as well as function, has concentrated on HLA-A and -B molecules because of their high sequence polymorphism and their dominating presence at the cell surface. In contrast, HLA-C molecules seemed to be of only minor importance in the cascade of immune reactions owing to their more limited polymorphism and reduced levels of surface expression. The inability to define a number of antigen specificities had the result that HLA-C molecules were often neglected in studies of immune response, transplantation, and disease association. More recently a new function has been identified for HLA class I molecules where they act as inhibitors of the lytic capacity of natural killer (NK) cells and non-MHC-restricted T-cells. Moreover, the understanding of this novel mode of negative regulation of cytotoxicity was remarkably influenced by HLA-C since these were the first HLA class I molecules found to have such inhibitory potential. With this new inhibitory function serving as an essential component of the immune system, HLA-C molecules can no longer be neglected.

HLA-B27 presents a peptide from a polymorphic region of its own molecule with homology to proteins from arthritogenic bacteria

A possible mechanism for the pathogenesis of HLA-B27-associated spondyloarthropathies is that peptides from arthritogenic bacteria with homology to endogenous self-peptides presented by HLA-B27, including those derived from HLA-B27 itself, could elicit an autoimmune T-cell response upon infection. We report here that an undecamer corresponding to the polymorphic region of HLA-B27 spanning residues 169-179 is presented in vivo by the B*2701, B*2704 and B*2706 subtypes, but was not detected in the B*2703-bound peptide pool. This peptide binds to B*2705 in vitro with sufficient affinity to allow its natural presentation by this subtype, but it binds with low affinity to B*2703. In spite of homology of this peptide to proteins from arthritogenic bacteria, its binding specificity does not correlate with current evidence concerning association of HLA-B27 subtypes to ankylosing spondylitis, suggesting that presentation of this peptide is not the critical feature that determines linkage of HLA-B27 to this disease.

Killer cell inhibitory receptor interactions with HLA class I molecules: implications for alloreactivity and transplantation

Human killer cell inhibitory receptors (KIR) are novel members of the immunoglobulin superfamily of cell surface glycoproteins, which are expressed by lymphocytes with natural killers (NK) and cytotoxic T-cell (CTL) phenotypes. These receptors have specificity for relatively conserved epitopes of HLA-A, -B, and -C class I antigens. Recent studies have identified KIR as being involved in the transmission of negative, inhibitory signaling events to the cytotoxic cell which prevent or diminish target cell lysis. KIR are thus likely to play an important role in the responses of alloreactive NK cells and CTL to allogeneic HLA antigens. In this article, we review the known structural and functional characteristics of KIR, suggest a possible mechanism for the transmission of intracellular negative signaling by these receptors, and discuss the relevance of KIR function and HLA specificity to the clinical transplantation of allogeneic tissues.

Presentation of HLA class I-derived peptides: potential involvement in allorecognition and HLA-B27-associated arthritis

Some 25 years ago, when purified HLA class I allotypes were first being analyzed, of major concern was that the papain used for solubilization might produce a mess of proteolytic fragments that would prove impossible to separate and sequence. Those fears proved unfounded (Parham et al. 1975), and the homogeneity of the preparations was sufficient to allow crystallization and determination of the three-dimensional structure (Bjorkman et al. 1987). Ironically the least ordered region of the electron density map provoked the most interest because it gave a first view of the diverse peptides bound by an MHC molecule. With this image a second chapter of HLA class I biochemistry began, its charge to determine the structures of bound peptides and their influence on the immune system. The extraordinary polymorphism of HLA class I heavy chains now seems quite manageable compared to the vast complexity of the peptides, and our present ignorance as to which ones are important for health and disease. The comparative weakness of most HLA class I associations with disease has made HLA-B27 an especially favored target for investigation, and more is known of the structure and peptide-presenting function of HLA-B27 than for any other HLA-B allotype (López de Castro 1994). Much of this information relates to the native HLA-B27 molecule and has been collected in the belief that disease is a direct consequence of its antigen-presenting function. If one subscribes to the relevance of the transgenic rodent models, this position has almost become untenable. For rats and mice 'non-functional' forms of HLA-B27 are the agents of disease, raising the possibility that B27-associated arthritis is induced by HLA class II presentation of a B27-derived peptide, a variant of the mechanism advanced for the classical HLA class II-associated diseases: type 1 diabetes, multiple sclerosis and rheumatoid arthritis (Gregersen et al. 1987, Roudier et al. 1989, Cucca & Todd 1996, Hall & Bowness 1996). Such speculation invites the obvious question as to whether other diseases associated with HLA class I and chronic inflammation, HLA-C and psoriasis for example (Tiilikainen et al. 1980, Yanagisawa et al. 1995), result from class II presentation of class I peptides.

Population genetic studies of HLA-G: allele frequencies and linkage disequilibrium with HLA-A1

HLA-G is a class I gene that is expressed in the extravillous cytotrophoblast. Although the function of this gene is still unknown, its expression at the maternal-fetal interface suggests that HLA-G may play a key role in the induction of tolerance during pregnancy. Preliminary to our studies of the effects of HLA-G polymorphisms on pregnancy outcome, we have defined HLA-G alleles in the Hutterites. We report here the presence of nine HLA-G alleles that differ with respect to nucleotide sequences, including four groups of alleles that differ with respect to amino acid sequences, and striking linkage disequilibrium between HLA-G and HLA-A alleles. The levels and sites of polymorphism in HLA-G suggest that this gene had a unique evolutionary history and may perform nonclassical functions at the maternal-fetal interface.

Binding of peptides naturally presented by HLA-B27 to the differentially disease-associated B*2704 and B*2706 subtypes, and to mutants mimicking their polymorphism

B*2704 and B*2706 are closely related HLA-B27 subtypes of which the former but not the latter is associated to ankylosing spondylitis. Their peptide specificity relative to other disease-associated subtypes was analyzed by testing binding of self-peptides naturally presented by B*2705 or B*2702, and synthetic analogs, to B*2704, B*2706, and site-specific mutants mimicking their changes. Peptides with basic, aliphatic or aromatic C-terminal residues bound to B*2705 with similar affinity. In B*2704 C-terminal aliphatic/ aromatic residues were preferred. B*2706 discriminated drastically between polar and nonpolar C-terminal residues, showing strong preference for Leu and Phe, and less than B*2704 for basic and Tyr residues. Loss of single acidic charges (D > S77, D > Y116) increased preference for C-terminal Leu and Phe, but allowed efficient binding of peptides with basic residues or Tyr. Their gain (V > E152, H > D114) maintained wide C-terminal specificity, but severely impaired binding, presumably by disrupting interactions with internal peptide residues. This was compensated by Y116 in the double D114Y116 mutant. The specificity of B*2704 and B*2706 was explained only partially by the separate effects of single mutations, indicating that novel properties arise from concomitant changes at various positions. For instance, specificity of B*2706 for nonpolar C-terminal residues required simultaneous removal of Asp77 and Asp116. B*2706 differed from B*2705, B*2702, and B*2704 in its lower suitability for C-terminal Tyr, suggesting that this feature might be relevant for HLA-B27 association to spondyloarthropathy.

Functions for MHC class I carbohydrates inside and outside the cell

Major histocompatibility complex (MHC) class I heavy chain glycoproteins have an invariant N-linked glycosylation site at Asn86, which is found between two extremely variable protein domains. For human MHC class I molecules, Asn is the only site of glycosylation and the attached oligosaccharides are remarkably uniform. The carbohydrate initiates interactions with calnexin in the endoplasmic reticulum that facilitate the assembly of MHC class I molecules and their delivery to the cell surface. However, recognition of MHC class I molecules by antibodies and T cells is indifferent to the carbohydrate, although lines of circumstantial evidence implicate lectins and carbohydrates in the recognition of MHC class I glycoproteins by natural killer cells.

A novel method for simultaneous high resolution identification of HLA-A, HLA-B, and HLA-Cw alleles

We describe a novel high resolution DNA based typing approach for HLA class I alleles, which identifies the recombinational motifs present in exons 2 and 3 of the HLA class I genes. Unique identification patterns for 201 known HLA-A, HLA-B, and HLA-Cw alleles were generated by the use of only 40 probes, which were targeted at these common motifs. The unambiguous identification of the alleles was achieved by the development of a new and powerful allelic separation technique that allows isolation of single alleles after amplification. To validate the method, we have used locus-specific primers to amplify exons 2 and 3 of HLA-A, HLA-B, and HLA-Cw loci from 22 heterozygous and 41 homozygous cell lines. After amplification, the allelic fragments from each locus were separated, blotted, and hybridized with the 40 probes. In all cases, the allelic products could be separated and 81 different class I alleles, 33 HLA-A, 30 HLA-B, and 18 HLA-Cw, were identified according to the predicted probe hybridization patterns.

Primary alloreactive cytotoxic T-lymphocytes are not commonly restricted by self-HLA class I antigens

To assess the role of HLA Class I molecules in the indirect presentation of alloantigen, we have investigated the fine specificity and MHC restriction of in vitro primary alloreactive cytotoxic T-lymphocytes (CTL), using limiting dilution analysis of CTL precursor frequencies in HLA-mismatched responder-stimulator pairs. By employing split-well analysis of limiting dilution (LD) microcultures and third-party target cells bearing a stimulatory HLA Class I antigen alone or in combination with a single responder HLA antigen, we demonstrate that self-Class I restriction of HLA-A- or HLA-B-specific CTL precursors is not a common feature of the primary in vitro alloresponse. Higher frequencies of alloantigen-specific CTL precursors in the presence of self-HLA antigens were only detected in 5 of 31 limiting dilution assays established from seven different responder-stimulator pairs. In two cases, the higher precursor frequencies could be explained on the basis of Class II-restricted presentation of Class I-derived antigenic peptide and are supported by flow cytometric analysis of HLA antigen expression on target cells. The remaining 3 assays of this type were suggestive of Class I restriction but revealed only marginally higher frequency estimates. All other LD assays revealed lower CTL precursor frequency estimates in the presence of self-HLA Class I antigens. A higher antigen-specific CTLp frequency was not detected when targets shared three HLA Class I antigens with the responder, demonstrating that we had not biased the responses by selecting single HLA antigen-sharing targets in the other assays. Analysis of reactivity against PHA blast targets at the single cell per well level demonstrated that CTL reactive only with the original stimulator comprised the majority of lytic reactions. Heteroclitic CTL (i.e., CTL that recognize single HLA targets only and not the original stimulator) formed only a small fraction of total reactivity. Our results confirm the role of Class II antigens in the indirect presentation of alloantigen in vitro but suggest that HLA Class I antigens play a limited role in this phenomenon.

Variation and evolution of class I Mhc in sexual and parthenogenetic geckos

We present the first Mhc class I sequences in geckos. We compared Mhc variation in gekkonid species that reproduce sexually (Hemidactylus frenatus, Lepidodactylus aureolineatus, L. moestus, L. sp. Arno, L. sp. Takapoto) to others reproducing parthenogenetically (H. garnotii, L. lugubris). These comparisons include the known maternal (L. moestus) and paternal (L. sp. Arno) ancestors of the asexual L. lugubris. Sequences similar to other vertebrate species were obtained from both nuclear and cDNA templates indicating that these sequences are derived from expressed class I Mhc loci. Southern blot analysis using gecko class I probes, revealed that parthenogenetic clonal lineages of independent evolutionary origin have no within-clone band variation at class I loci and that no detectable recombination between restriction sites had taken place. Variability in the sexual species was similar to mammalian taxa, i.e. class I genes are highly variable in outbreeding sexual populations. Sequence analysis of the alpha-2 domain of class I genes identified point mutations in a clonal lineage of L. lugubris which led to amino acid substitutions. Potential transspecific allelic lineages were also observed. The persistence of asexual lineages with little or no class I diversification over thousands of generations seems to argue against strong selection for Mhc multi-allelism caused by pathogen-Mhc allele specificity. On the other hand, the high level of heterozygosity in the parthenogenetic species (a consequence of their hybrid origin) may provide clonal lineages with adequate antigen presenting diversity to survive and compete with sexual relatives.

The inter-locus recombinant HLA-B*4601 has high selectivity in peptide binding and functions characteristic of HLA-C

The vast majority of new human HLA class I alleles are formed by conversions between existing alleles of the same locus. A notable exception to this rule is HLA-B*4601 formed by replacement of residues 66-76 of the alpha 1 helix of B*1501 by the homologous segment of Cw*0102. This inter-locus recombination, which brings together characteristic elements of HLA-B and HLA-C structure, is shown here to influence function dramatically. Naturally processed peptides bound by B*4601 are distinct from those of its parental allotypes B*1501 and Cw*0102 and dominated by three high abundance peptides. Such increased peptide selectivity by B*4601 is unique among HLA-A,B,C allotypes. For other aspects of function, presence of the small segment of HLA-C-derived sequence in an otherwise HLA-B framework converts B*4601 to an HLA-C-like molecule. Alloreactive cytotoxic T lymphocytes (CTL), natural killer (NK) cells, and cellular glycosidases all recognize B*4601 as though it were an HLA-C allotype. These unusual properties are those of an allotype which has frequencies as high as 20% in south east Asian populations and is associated with predisposition to autoimmune diseases and nasopharyngeal carcinoma.

Homocysteine modification of HLA antigens and its immunological consequences

Homocysteine-treated cells can be specifically lysed by cytotoxic T lymphocytes (CTL) identifiable in patients with ankylosing spondylitis and reactive arthritis. Sensitization of target cells involves disulfide bonding and the interaction between homocysteine and HLA antigens occurs in a pre-Golgi compartment in the cells. Salmonella-infected B cells are also lysed by homocysteine-specific CTL, suggesting that intracellular invading microorganisms may provide homocysteine which would gain access to the newly synthesized intracellular HLA molecules and modify them inside the cells. Two different mechanisms for homocysteine modification of HLA antigens are proposed: homocysteine could bind directly to the unpaired cysteine residues in HLA antigens, or it could bind indirectly to HLA antigens through cysteine-containing peptides bound to them. Thus, HLA antigens containing unpaired cysteine residues (e.g. HLA B27) could be modified by homocysteine directly or indirectly, while HLA antigens without unpaired cysteine residues (e.g. HLA A68) could only be modified indirectly. The results are discussed in relation to the potential involvement of homocysteine-specific CTL in ankylosing spondylitis and reactive arthritis, both of which are related to bacterial infections, associated with HLA B27, and considered to be autoimmune diseases.

Characterization of the peptide-binding specificity of HLA-B*7301

Previous studies showed the human MHC class I heavy chain HLA-B*7301 has a sequence very divergent from other class I alleles. Despite the unusual sequence, we predicted B*7301 would retain the peptide-binding function typical of other HLA-A, B and C glycoproteins, and sequence similarity to B*2705 in a region of the peptide-binding site known as the B pocket suggested B*7301 would bind peptides with Arg at position 2. To test this hypothesis, the peptide-binding specificity of B*7301 was investigated. Sequence analysis of peptides bound endogenously by B*7301 indeed found selectivity for nonamer peptides possessing Arg at position 2 and a preference for small nonpolar residues such as Pro or Ala at the C terminus was also revealed. B*7301 therefore possesses the potential to function as a conventional antigen presenting class I glycoprotein. Functional similarities between B*7301 and B*2705 are discussed in the context of the association of B*27 subtypes with susceptibility to ankylosing sponylitis and arthritic diseases.

Identification of new TAP2 alleles in gorilla: evolution of the locus within hominoids

Transporters associated with antigen processing molecules (TAP1 and TAP2) mediate the transfer of cytosolic peptides into the lumen of the endoplasmic reticulum for association with newly synthesized class I molecules of the major histocompatibility complex. Previous molecular and functional analyses of rat and human TAP2 homologues indicated major differences in gene diversification patterns and selectivity of peptides transported. Therefore, in this study, we analyzed the alleles of the gorilla TAP2 locus to determine whether the pattern of diversification resembled that in either of those two species. Sequence analysis of the TAP2 cDNAs from gorilla Epstein-Barr virus-transformed B-cell lines revealed four alleles with a genetic distance of less than 1%. The nucleotide substitutions distinguishing the alleles are confined to the 3' half of the coding region and occur individually or within two small clusters of variability. Diversification of the locus appears to have resulted from point substitutions and recombinational events. Evolutionary-rate estimates for the TAP2 gene in gorilla and human closely approximate those observed for other hominoid genes. The amino acid polymorphisms within the gorilla molecules are distinct from those in the human homologues. The absence of ancestral polymorphisms suggests that gorilla and human TAP2 genes have not evolved in a trans-species fashion but rather have diversified since the divergence of the lineages.

Characterization of baboon class I major histocompatibility molecules. Implications for baboon-to-human xenotransplantation

Increasingly strong medical and political pressures are stimulating consideration of the transplantation of baboon organs and cells into humans. Critical to the success of these xenotransplants is management of the immune system such that graft rejection and, in the case of bone marrow transplantation, graft-versus-host disease do not result in transplant failure. The polymorphic products of the major histocompatibility complex (MHC) are the primary barrier to successful allotransplantation, and here we describe class I MHC molecules from baboon (Papio anubis) to gain an understanding of how similarities and differences between baboon and human MHC molecules might affect xenograft survival and function. Comparative analyses of our five novel baboon class I molecules with defined HLA class I molecules demonstrate that the baboon class I molecule are up to 90% identical. Disparity between baboon class I proteins and their human homologues lies predominately at positions in the antigen-binding groove, while C-terminal portions of the class I heavy chain are more conserved between the two species. Such concentration of cross-species differences within the alpha1 and alpha2 domains involves a majority of substitutions at positions demonstrating polymorphism in human alleles; the location of substitutions distinguishing baboon and human molecules thus resembles the positioning of human class I allopolymorphisms. Because this preliminary characterization indicates that both baboon and human T cells with be restricted by xenogeneic class I molecules, immune responses triggered during baboon-to-human transplantation should mimic those arising during MHC mismatched human allotransplantation.

Antigen processing and presentation by the class I major histocompatibility complex

Major histocompatibility complex (MHC) class I molecules bind peptides derived from cellular proteins and display them for surveillance by the immune system. These peptide-binding molecules are composed of a heavy chain, containing an antigen-binding groove, which is tightly associated with a light chain (beta 2-microglobulin). The majority of presented peptides are generated by degradation of proteins in the cytoplasm, in many cases by a large multicatalytic proteolytic particle, the proteasome. Two beta-subunits of the proteasome, LMP2 and LMP7, are inducible by interferon-gamma and alter the catalytic activities of this particle, enhancing the presentation of at least some antigens. After production of the peptide in the cytosol, it is transported across the endoplasmic reticulum (ER) membrane in an ATP-dependent manner by TAP (transporter associated with antigen presentation), a member of the ATP-binding cassette family of transport proteins. There are minor pathways for generating presented peptides directly in the ER, and some evidence suggests that peptides may be further trimmed in this location. The class I heavy chain and beta 2-microglobulin are cotranslationally translocated into the endoplasmic reticulum where their assembly may be facilitated by the sequential association of the heavy chain with chaperone proteins BiP and calnexin. The class I molecule then associates with the lumenal face of TAP where it is retained, presumably awaiting a peptide. After the class I molecule binds a peptide, it is released for exocytosis to the cell surface where cytotoxic T lymphocytes examine it for peptides derived from foreign proteins.

Further molecular diversity in the HLA-B15 group

In order to further clarify the diversity of the HLA-B15 antigens and the correspondence of serological types with alleles in Asians, we screened various B15 serological splits by means of a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method. Subsequently, the genes encoding various B15 variants were sequenced. Two novel alleles, B*1528 and B*1529, were identified: the nucleotide sequence of the former contained a single-base substitution at position 263 in exon 2 as compared to that of the B*1501 allele, which results in an amino acid change at position 64 in the alpha 1 domain, and the nucleotide sequence of the latter differs from that of B*1518 by a single-base substitution at position 272 of exon 2 which results in an amino acid change at position 67 of the alpha 1 domain. One new allele, B*1521, described recently in Australian Aborigines was also identified in Asians in the present study. Moreover, the results of sequencing demonstrated that Asian HLA-B62, B70, and B77 antigens are encoded by B*1501, B*1518, and B*1513, respectively. Two splits of B75 antigens, B75V (TS-1) and B15N, which have been proposed to exist in the Japanese population were encoded by B*1511 and B*1502, respectively. Most of the B15 alleles detected in the present study showed positive associations with other locus antigens. Especially, B*1502 was strongly associated with Cw8, while B*1521 was strongly associated with A34 and Cw6.

HLA-B40, B18, B27, and B37 allele discrimination using group-specific amplification and SSCP method

We developed a system for discriminating HLA-B40, B18, B27, and B37 alleles using a two-step PCR method followed by SSCP analysis. Fragments (0.8 kb) including exon 2, intron 2, and exon 3 were amplified in the first PCR. We used two sets of primers, one specific for HLA-B60-related alleles and the other specific for HLA-B61-related, B18, B27, and B37 alleles. No amplifications of other class I genes or pseudogenes were observed. In the second PCR, exon 2 and exon 3 were amplified separately, using diluents of the first PCR products as templates. HLA-B61-related, B18, B27, B37, and B60-related alleles were clearly discriminated in the SSCP analysis of the second PCR products. In a population study in which B61 alleles were analyzed, B*4003 was detected in two Japanese individuals in addition to two B61 alleles previously reported to occur in Japanese, B*4002 and B*4006. The relative frequencies of B*4002, B*4006, and B*4003 in Japanese were 58, 35, and 6%, respectively. The individuals having B*4003 are the first non-South Americans in whom this allele has been detected. The SSCP banding patterns of 18 HLA-B60-positive Japanese population samples were identical to those of a B*40012 sample for both exon 2 and exon 3. We also demonstrated that the B37 allele occurring in some Japanese is B*3701.

Definition of an HLA-A3-like supermotif demonstrates the overlapping peptide-binding repertoires of common HLA molecules

An HLA-A3-like supertype (minimally comprised of products from the HLA class I alleles A3, A11, A31, A*3301, and A*6801) has been defined on the basis of (a) structural similarities in the antigen-binding groove, (b) shared main anchor peptide-binding motifs, (c) the identification of peptides cross-reacting with most or all of these molecules, and (d) the definition of an A3-like supermotif that efficiently predicts highly cross-reactive peptides. Detailed secondary anchor maps for A3, A11, A31, A*3301, and A*6801 are also described. The biologic relevance of the A3-like supertype is indicated by the fact that high frequencies of the A3-like supertype alleles are conserved in all major ethnic groups. Because A3-like supertype alleles are found in most major HLA evolutionary lineages, possibly a reflection of common ancestry, the A3-like supermotif might in fact represent a primeval human HLA class I peptide-binding specificity. It is also possible that these phenomena might be related to optimal exploitation of the peptide specificity by human TAP molecules. The grouping of HLA alleles into supertypes on the basis of their overlapping peptide-binding repertoires represents an alternative to serologic or phylogenetic classification.

B27 polymorphism and peptide repertoire

Over 130 HLA-B alleles have been defined at the level of nucleotide sequence. Nine of these are subtypes of HLA-B27. To understand how HLA-B27 predisposes towards arthritis it is important to determine which B27 subtypes are associated with disease susceptibility and which are not. A characteristic of HLAB27 is the binding of peptides having arginine at position 2. However, HLA-B*7301, a rare and unusual allele of European populations, has an identical "B" subpocket to B*27 and also binds peptides with arginine at position 2. The association of the Bw4 public epitope with inhibition of certain NK cells raises the possibility that NK cell responses may contribute to HLA-B27-associated disease.

Novel alleles HLA-B*7802 and B*51022: evidence for convergency in the HLA-B5 family

We have characterized two novel HLA-B alleles, B*7802 and B*51022. The Caucasian-derived variant B*7802 most resembles the African-derived variant B*7801, from which B*7802 differs by two nucleotides. Only one of these modifications, however, is translated: a tyrosine for aspartate substitution occurs at residue 74 in B*7802, while the second nucleotide difference reflects a proximal synonymous substitution in codon 23. A second variant, B*51022, differs synonymously only at codon 23 from B*51021. Comparative analysis of the B5 CREG demonstrates that other pairs of B5 alleles differ synonymously only at codon 23 or synonymously at codon 23 and non-synonymously at a second more distal location. Contrary to the genesis of like pairs of B5 alleles via introduction of coordinate yet distant mutagenic events onto a single B5 progenitor, we postulate that synonymously different B5 progenitor molecules, B5ATT and B5ATC, are evolving in convergence to generate homologous B5 allele pairs differing silently at codon 23. Our finding that B*7802 is a single amino acid away from complete convergence with B*7801 and that B*51022 and B*51021 are in complete convergence is exemplary of such evolution.

Binding of nonamer peptides to three HLA-B51 molecules which differ by a single amino acid substitution in the A-pocket

The interaction between 9-mer peptides and HLA-B51 molecules was investigated by quantitative peptide binding assay using RMA-S cells expressing human beta2-microglobulin and HLA-B51 molecules. Of 147 chemically synthesized 9-mer peptides possessing two anchor residues corresponding to the motif of HLA-B*5101 binding self-peptides, 27 peptides bound to HLA-B*5101 molecules. Pro and Ala at position 2 as well as Ile at position 9 were confirmed to be main anchor residues, while Gly at position 2 as well as Val, Leu, and Met at position 9 were weak anchor residues for HLA-B*5101. The A-pocket is suspected to have a critical role in peptide binding to MHC class I molecules because this pocket corresponds to the N-terminus of peptides and has a strong hydrogen bond formed by conserved Tyr residues. Further analysis of peptide binding to HLA-B*5102 and B*5103 molecules showed that a single amino acid substitution of Tyr for His at residue 171(B*5102) and that of Gly for Trp at residue 167 (B*5103) has a minimum effect in HLA-B51-peptide binding. Since previous studies showed that some HLA-B51 alloreactive CTL clones failed to kill the cells expressing HLA-B*5102 or HLA-B*5103, these results imply that the structural change of the A-pocket among HLA-B51 subtypes causes a critical conformational change of the epitope for TCR recognition rather than influences the interaction between peptides and MHC class I molecules.

The enigma of the natural killer cell

Natural killer (NK) cells are controlled by receptors specific for polymorphic determinants of class I molecules of the major histocompatibility complex (MHC). The contrasting properties of NK and cytotoxic T cell (CTL) class I receptors provide complementarity in the cytolytic lymphocyte response to viruses, tumours and transplants. Whereas human NK cell class I receptors consist of immunoglobulin domains, their mouse counterparts resemble C-type lectins. This difference may reflect the receptors' diverse and rapidly evolving class I ligands.

Low HLA-C expression at cell surfaces correlates with increased turnover of heavy chain mRNA

In comparison with HLA-A and -B, the protein products of the HLA-C locus are poorly characterized, in part because of their low level of expression at the cell surface. Here, we examine how protein-protein interactions during assembly and regulation of the mRNA level affect cell surface expression of HLA-C. We find that intrinsic properties of the HLA-C heavy chain proteins do not correlate with low cell surface expression: HLA-C heavy chains associate and dissociate with beta 2-microglobulin (beta 2m) at rates comparable to those found for HLA-A and -B, and increased competition for beta 2m does not alter the surface expression of HLA-C. From studies of chimeric genes spliced from the HLA-B7 and -Cw3 genes, we find that chimeric proteins containing the B7 peptide-binding groove can have low cell surface expression, suggesting that inefficiency in binding peptides is not the cause of low cell surface expression for HLA-C. The surface levels of HLA-A, -B, or -C in cells transfected with cDNA can be similar, implicating noncoding regions of HLA-C heavy chain genes in the regulation of surface expression. We find that HLA-C mRNA is expressed at lower levels than HLA-B mRNA and that this difference results from faster degradation of the HLA-C message. Experiments examining chimeric B7/Cw3 and B7/Cw6 genes suggest that a region determining low expression of HLA-C is to be found between the 3' end of exon 3 and a site in the 3' untranslated region, approximately 600 bases downstream of the translation stop codon.

Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes

BACKGROUND

Polymorphism among class I molecules of the major histocompatibility complex (MHC) confers allotypic specificity on the peptides that these molecules bind and present to cytotoxic T lymphocytes. Evolution of new human HLA class I alleles usually involves gene recombination events that replace a segment of one allele with the homologous region of another. In this study, the impact of these evolutionary changes has been assessed by comparison of the peptide-binding specificities of six related HLA-B allotypes.

RESULTS

Endogenous peptides bound by HLA-B*5401, HLA-B*5501, HLA-B*5502, HLA-B*5601, HLA-B*6701 and HLA-B*0702 were characterized. Despite differing by 1-9 of the amino-acid residues comprising their peptide-binding sites, all these allotypes share a dominant preference for peptides that have proline at position 2. Polymorphism results in differing selection of carboxy-terminal and secondary anchor residues, but the peptide-binding specificities are sufficiently similar that there is overlap in the repertoires of peptides bound by these allotypes. Complete sequence determination of individual peptides revealed four that could be isolated from two or more allotypes. Members of the closely related HLA-B22 family--HLA-B*5401, HLA-B*5501, HLA-B*5502 and HLA-B*5601--show only minor differences in their peptide-binding specificities. This marked similarity is reflected at the functional level, as alloreactive cytotoxic T lymphocytes generated against HLA-B*5401 and HLA-B*5501 exhibited cross-reactive recognition.

CONCLUSION

The isolation of identical endogenously bound peptides from six HLA-B allotypes demonstrates overlap in the repertoires of peptides bound in vivo by different allotypes. We speculate that the shared preference for binding peptides with proline at position 2 reflects a selective pressure to retain this specificity, which may be based upon peptide availability in vivo. Characterization of the overlap between the repertoires of peptides bound by HLA-B allotypes could simplify the development of peptide-based vaccines that are targeted to cytotoxic T cells, as single peptides would be effective for humans of different HLA types.