Molecular analysis of HLA-DRB1*08/12 alleles: identification of two additional alleles

HLA class II peptide-binding-region analysis reveals funneling of polymorphism in action

BACKGROUND

HLA-class II proteins hold important roles in key physiological processes. The purpose of this study was to compile all class II alleles reported in human population and investigate patterns in pocket variants and their combinations, focusing on the peptide-binding region (PBR).

METHODS

For this purpose, all protein sequences of DPA1, DQA1, DPB1, DQB1 and DRB1 were selected and filtered, in order to have full PBR sequences. Proportional representation was used for pocket variants while population data were also used.

RESULTS

All pocket variants and PBR sequences were retrieved and analyzed based on the preference of amino acids and their properties in all pocket positions. The observed number of pocket variants combinations was much lower than the possible inferred, suggesting that PBR formation is under strict funneling. Also, although class II proteins are very polymorphic, in the majority of the reported alleles in all populations, a significantly less polymorphic pocket core was found.

CONCLUSIONS

Pocket variability of five HLA class II proteins was studied revealing favorable properties of each protein. The actual PBR sequences of HLA class II proteins appear to be governed by restrictions that lead to the establishment of only a fraction of the possible combinations and the polymorphism recorded is the result of intense funneling based on function.

Peanut-allergic subjects and their peanut-tolerant siblings have large differences in peanut-specific IgG that are independent of HLA class II

We enrolled 53 peanut-allergic subjects and 64 peanut-tolerant full siblings, measured peanut-specific IgG and IgE, determined HLA class II at high resolution, and analyzed DRB1 alleles by supertypes. Peanut-specific IgG and IgE were elevated in the peanut-allergic subjects (p<0.0001) but did not stratify with HLA alleles, haplotypes, or supertypes. There were no significant differences in HLA class II between the peanut-allergic and peanut-tolerant siblings but there was an increased frequency of DRB1*0803 in both sets of siblings compared to unrelated controls (p(c)=4.5×10⁻⁹). Furthermore, we identified 14 sibling pairs in which the peanut-allergic and the peanut-tolerant siblings have identical HLA class II and again found an elevation of anti-peanut IgG in the peanut-allergic subjects (p<0.0001). In conclusion, although DRB1*0803 may identify a subset of families with increased risk of peanut allergy, differences in peanut-specific immunoglobulin production between peanut-allergic subjects and their peanut-tolerant siblings are independent of HLA class II.

A deletion in the second exon of an HLA-DRB1 allele found in a DR2-negative narcolepsy patient

In this report, we describe a new allele of the HLA-DRB 1 gene carrying a form of mutation that has not been observed before. It appeared in an HLA-DR2-negative narcolepsy patient who, besides HLA-DR4, revealed a serologic HLA-DR blank segregating with HLA-DQ1. Oligotyping showed that the new allele belongs to the HLA-DR8 group. Restriction analysis and DNA sequencing revealed the deletion of 12 bp as well as the substitution of 9 flanking base pairs between codons 36 and 43. The expression of the mutated gene was demonstrated by the presence of its messenger RNA and a few positive reactions with DR8 sera. Without interrupting the reading frame, the mutation leads to a gene product composed of a modified amino acid sequence. We anticipate that the mutation influences the conformation of the molecule with possible consequences concerning immune response.

Two new HLA DRB1 alleles found in African Americans: implications for balancing selection at positions 57 and 86

Two new DRB1 alleles have been identified (DRB1*0303 and DRB1*0805) in African Americans that differ from known DRB1 alleles only by a glycine to valine exchange at position 86. The novel DRB1*0303 allele, found in one individual, has the same DQA1*0401-DQB1*04 haplotype as DRB1*0302, suggesting that it may be a recent diversification of *0302. The novel DRB1*0805 allele, identified in 4 individuals, was found on two haplotypes, sharing a DQA1*0501-DQB1*0301 haplotype with DRB1*0804, and a DQA1*0102-DQB1*0602 haplotype found with DRB1*0801 in some African populations. DRB1*0805 differs from *0804 only at position 57 and differs from *0801 only at position 86. Assuming that DRB1*0801 and DRB1*0802 are ancestral, based on their distribution in various human populations, DRB1*0805 may have been generated twice by two independent mutations or gene conversion events at each of these positions. Alternatively, DRB1*0805 may have arisen from a single gene conversion event (or mutation) and recombined to generate multiple DR-DQ haplotypes. These findings increase the number of DRB1 allelic pairs that differ only at position 86 to 9, suggesting strong balancing selection at this position. A number of DRB1 alleles for DR8 and DR4 also differ only at position 57, a site previously postulated to be strongly influenced by balancing selection in DQB1 alleles by phylogenetic analysis.