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

HLA class I and beta-2-microglobulin (beta 2m) expression in a moderately d ifferentiated laryngeal squamous cell carcinoma appeared to be downregulate d when analyzed by immunohistochemical procedures using the monomorphic ant i-HLA class I monoclonal antibody (mAb; W6/32), locus-specific (HCA2 and HC 10) and allele-specific (LT129.11 and KRE501) mAbs and anti-beta 2m mAbs. T o 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*31 012 allele, which lacked all introns when sequenced from the initiation cod on through exon eight. The 3' UTR region was intact up to at least 200 bp d ownstream. The mutant HLA-A*31012 is restricted to laryngeal tumor tissue s ince it was not amplified in flanking tumor-free laryngeal tissue. The muta nt HLA-A*31012 shares structural characteristics with processed pseudogenes , i.e., absence of introns and an intact 3' UTR. This indicates that the mu tant HLA-A*31012 allele resulted from a retroposition (reverse transcriptio n and integration) from the processed transcript of the wild-type HLA-A*310 12 allele within a clonal tumor cell. Genes Chromosomes Cancer 27:26-34, 20 00. (C) 2000 Wiley-Liss, Inc.