Identification of 4 different alternatively spliced HLA-A transcripts

During the development of a sequencing based typing (polymerase chain reaction (PCR)-SBT) protocol for the HLA-A locus, the presence of two bands in addition to the expected full-length product were observed in the template generating PCR in some of the samples investigated. Despite a profound optimisation of the PCR, these new products of lower molecular weight remained present. The new products were not associated with specific alleles. However, the affected samples consisted of peripheral blood lymphocytes isolated from four patients with colorectal cancer, one patient diagnosed with myeloma, and a colon tumor cell line. In order to elucidate the nature of this phenomenon, a number of these products were cloned and sequenced. Sequence analysis revealed that alternative splicing of the HLA-A transcript was responsible for the generation of these smaller products. Thus, a number of clones were generated from transcripts in which a 276 base pair region corresponding exactly to exon 3 had been spliced out. Three additional transcripts lacking exons 2 and 3, exons 3 and 4, and transcripts lacking exons 2-4 respectively, were identified as well. These results are in some respects similar to observations made for HLA-G, one of the nonclassical class I loci, in which a number of alternatively spliced transcripts have been identified. However, no specific functions have been ascribed to these molecules nor have the truncated proteins encoded by these transcripts been identified, thereby questioning the biological significance of these observations. Nevertheless, our findings indicate that alternative splicing of the HLA-A transcript may take place to a small extent in virtually all cells, and it is possible that their generation promote escape from immune surveillance.