Cloning and analysis of HLA class I cDNA encoding a new HLA-C specificity Cx52

HLA-C loci frequently have an unclassifiable "blank (CwBL)" specificity. It is unclear whether HLA-C specificities associated with the haplotypes of A24 Bw52 CwBL DR2 DQw1 and Aw33 B44 CwBL DRw13 DQw1 in Japanese (tentatively named Cx52 and Cx44, respectively) really exist. Southern hybridization experiments revealed that restriction enzyme-cleaved genomic DNA from AKIBA, consanguineous HLA homozygote, two other homozygotes with the former haplotype, and three homozygous cells with the latter haplotype hybridized strongly with an HLA-C-specific probe. We have screened the cDNA library constructed from AKIBA to isolate cDNA clones encoding the putative Cx52 antigen, and picked up 103 cDNA clones with HLA-class I DNA probes as possible candidates. By restriction enzyme mapping and Southern hybridization of selected clones, we identified three isotypes of cDNA clones, pA01, pB55, and pC68, which appeared to encode A24, Bw52, and Cx52, respectively. The nucleotide sequence of pC68 showed higher homology with exons of the HLA-C gene than with those of the HLA-A and HLA-B genes, especially in exons 6-8 which include the HLA-C-specific region. Comparison of amino acid sequences showed more than 86% homology among Cw1, Cw2, Cw3, and new pC68-encoded Cx52 proteins. These results support the notion that the inability to define C antigens serologically in this Cx52 haplotype is not due to a HLA-C gene deletion or mutation, but to the absence of typing sera.