Detection of a putative HLA-A*31012 processed (intronless) pseudogene in a laryngeal squamous cell carcinoma

HLA class I and beta-2-microglobulin (beta2m) expression in a moderately differentiated laryngeal squamous cell carcinoma appeared to be downregulated when analyzed by immunohistochemical procedures using the monomorphic anti-HLA class I monoclonal antibody (mAb; W6/32), locus-specific (HCA2 and HC10) and allele-specific (LT129.11 and KRE501) mAbs and anti-beta2m mAbs. To reveal the molecular basis of downregulated HLA class I expression, HLA-A typing was performed on DNA derived from peripheral blood lymphocytes (PBL) and the tumor. Sequencing-based typing (SBT) revealed HLA-A*02011, 31012. In addition to HLA-A*02011, 31012 alleles, the tumor contained an HLA-A*31012 allele, which lacked all introns when sequenced from the initiation codon through exon eight. The 3' UTR region was intact up to at least 200 bp downstream. The mutant HLA-A*31012 is restricted to laryngeal tumor tissue since it was not amplified in flanking tumor-free laryngeal tissue. The mutant HLA-A*31012 shares structural characteristics with processed pseudogenes, i.e., absence of introns and an intact 3' UTR. This indicates that the mutant HLA-A*31012 allele resulted from a retroposition (reverse transcription and integration) from the processed transcript of the wild-type HLA-A*31012 allele within a clonal tumor cell. Genes Chromosomes Cancer 27:26-34, 2000.