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The HLA-B*53:69 allele differs from HLA-B*53:01:01:01 by two nucleotide changes in exon 3., (© 2023 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

One nucleotide substitution in codon 112 of HLA-B*15:349:01 results in a novel allele, HLA-B*15:349:02., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

One nucleotide substitution in codon 89 of HLA-B*38:02:01:01 results in a novel allele, HLA-B*38:64., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

DNA substitutions from codons 69 to 71 of HLA-B*35:05:01:01 result in a novel allele, HLA-B*35:368., (© 2020 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Nucleotide substitutions at residues 105 and 106 of HLA-B*58:01:01:01 result in a novel allele, HLA-B*58:74., (© 2019 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

HLA class I glycoproteins contain the functional sites that bind peptide antigens and engage lymphocyte receptors. Recently, clinical application of sequence-based HLA typing has uncovered an unprecedented number of novel HLA class I alleles. Here we define the nature and extent of the variation in 3,489 HLA-A, 4,356 HLA-B and 3,111 HLA-C alleles. This analysis required development of suites of methods, having general applicability, for comparing and analyzing large numbers of homologous sequences. At least three amino-acid substitutions are present at every position in the polymorphic α1 and α2 domains of HLA-A, -B and -C. A minority of positions have an incidence >1% for the 'second' most frequent nucleotide, comprising 70 positions in HLA-A, 85 in HLA-B and 54 in HLA-C. The majority of these positions have three or four alternative nucleotides. These positions were subject to positive selection and correspond to binding sites for peptides and receptors. Most alleles of HLA class I (>80%) are very rare, often identified in one person or family, and they differ by point mutation from older, more common alleles. These alleles with single nucleotide polymorphisms reflect the germ-line mutation rate. Their frequency predicts the human population harbors 8-9 million HLA class I variants. The common alleles of human populations comprise 42 core alleles, which represent all selected polymorphism, and recombinants that have assorted this polymorphism.

We have identified a dimorphic site in intron 1 of the HLA-B gene. Oligotyping was performed on about 3000 samples using primers derived from this dimorphic site in combination with a locus-specific primer derived from intron 3. The distribution of B-alleles bearing each of the dimorphic sequences was approximately equal. These primers were mutually exclusive and yielded approximately 50% of the heterozygous samples as apparently homozygous in PCR products. Intermediate and almost high-resolution oligotyping of HLA-B alleles was achieved using 35 and 63 hybridization probes, respectively. This dimorphic site will provide a useful tool for other PCR-based HLA-B typing approaches.

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.

Alloreactivity against micromismatches in MHC class I molecules is difficult to measure. Here, we describe an in vitro model with which it is possible to examine alloreactivity against a single HLA class I allotype. The HLA class I- and class II-negative myelocytic leukemia cell line K562 was transfected with a genomic DNA clone carrying B*4403 to express a single allotype. CTL lines were generated from normal individuals carrying B*4402, B*4403, or unrelated HLA-B alleles by stimulation with B*4403- transfected K562. The bulk CTL lines generated from B*4402+ T cells against B*4403 that carry a single amino acid disparity at position 156 were specific for B*4403+ targets and did not react with targets carrying any other HLA allotype. However, the CTL lines generated from B44-negative individuals exhibited killing of the targets bearing not only B44, but also B44 CREG and a few other B alleles. Reverse transcriptase-PCR analysis of TCRs, expressed in the CTL clones uniquely specific for B*4403, showed that TCR V beta usage of alloreactive T cells directed against B*4403 was diverse but nonrandom and was affected by the HLA background of the responder. Thus, the K562-HLA transfectant system provides a useful in vitro tool to analyze alloreactivity against a single class I allele and to aid in the prediction of alloreactivity in unrelated marrow transplantation.

We have identified locus-specific sequences in the first and third introns flanking the polymorphic second and third exons of HLA class I genes. PCR primers derived from these conserved sequences produced DNA fragments of the expected sizes for each of the HLA-A, -B, and -C loci in the amplification of genomic DNA. PCR products generated using each of the locus-specific sets of primers displayed exquisite locus specificity, as assessed by hybridization with oligonucleotide probes specific for ten classical and non-classical HLA class I genes. Amplification with these primer sets was effective and specific for the HLA alleles tested under the given PCR conditions. When hybridized with oligonucleotides derived from shared polymorphic sequence motifs, reaction patterns of PCR products from each locus were precisely as expected from published or database sequences. Chemiluminescent signals generated from digoxygenin-ddUTP-labeled probes were even for all samples and as strong as those obtained in MHC class II typing. These locus-specific primer sets derived from intron sequences provide an effective means to amplify genomic DNA which will facilitate PCR-based HLA class I typing methods. This will also allow HLA class I typing to be conducted with greater precision, at lower cost, and faster than previously described class I typing methodologies.

Recently, we have demonstrated that the HLA class I regulatory complex (CRC) is conserved in a locus-specific manner with limited allelic variation. In this study, we have analyzed the CRC sequences of the alleles that showed variation from a total of 22 well-characterized, HLA-homozygous B-LCLs, using PCR amplification of genomic DNA and direct sequencing. We compared the sequences of these alleles with their respective locus consensus sequence at kappa B1, kappa B2, the IRS, the putative NRE, and the HLA counterpart of the H-2RII region, the R x R beta-binding site. The palindromic kappa B1 sequence, an active enhancer, was found to be conserved in all HLA-A and -B alleles and in one HLA-C allele. The sequences of the kappa B2 site showed locus-specific divergence with almost no allelic variation. The IRS is strictly locus specific and HLA-B and -C have identical sequences in this region. Variation in the putative NRE sequence and RII-kappa B2 junctional sequence was apparently generated by gene conversion between B and C loci. Each locus had two sequence patterns at the putative RII site. Overall, sequence analysis of variant alleles demonstrated that there is limited variation in a nonrandom fashion. These results may provide a structural basis for locus and allele-specific modulation of these genes.