Identification of 4 different alternatively spliced HLA-A transcripts

During the development of a sequencing based typing (polymerase chain react ion (PCR)SBT) protocol for the HLA-A locus, the presence of two bands in ad dition to the expected full-length product were observed in the template ge nerating PCR in some of the samples investigated. Despite a profound optimi sation of the PCR, these new products of lower molecular weight remained pr esent. The new products were not associated with specific alleles. However, the affected samples consisted of peripheral blood lymphocytes isolated fr om four patients with colorectal cancer. one patient diagnosed with myeloma , and a colon tumor cell line. In order to elucidate the nature of this phe nomenon, a number of these products were cloned and sequenced Sequence anal ysis revealed that alternative splicing of the HLA-A transcript was respons ible for the generation of these smaller products. Thus, a number of clones were generated from transcripts in which a 276 base pair region correspond ing exactly to exon 3 had been spliced out. Three additional transcripts la cking exons 2 and 3, exons 3 and 4, and transcripts lacking exons 2-4 respe ctively, were identified as well. These results are in some respects simila r to observations made for HLA-G, one of the nonclassical class I loci in w hich a number of alternatively spliced transcripts have been identified. Ho wever, no specific functions have been ascribed to these molecules nor have the truncated proteins encoded by these transcripts been identified, there by questioning the biological significance of these observations. Neverthel ess, our findings indicate that alternative splicing of the HLA-A transcrip t may take place to a small extent in virtually all cells. and it is possib le that their generation promote escape from surveillance.