Translisin recognition site sequences flank translocation breakpoints in a Philadelphia chromosome positive chronic myeloid leukemia patient expressing a novel type of chimeric BCR-ABL transcript (E8-INT-A2)

Comprehensive characterization of a novel intronic pseudo-exon inserted within an e14/a2 BCR-ABL rearrangement in a patient with chronic myeloid leukemia

We identified a novel breakpoint cluster region-ABL rearrangement in a chronic myeloid leukemia (CML) patient. The e14/a2 (b3/a2) type BCR-ABL mRNA incorporated a 42-nucleotide intronic insertion of ABL intron Ib between BCR exon e14 and ABL exon a2. As we hypothesized that the rearrangement between BCR and ABL genes occurred near the inserted sequence and because of the relative small size of BCR intron 14, we determined the BCR-ABL breakpoint at the genomic DNA level. Using a PCR-based method, this analysis revealed that i) BCR intron 14 brought a potential lariat branch point and the polypyrimidine tract, ii) the BCR-ABL breakpoint created a chimeric acceptor site, and iii) the inserted sequence of ABL intron Ib carried at its 3' end a well-conserved donor splice site. Therefore, the inserted sequence was flanked by canonical consensus splice sites and recognized as a pseudo-exon (as shown by splice site prediction and exon finder software). Moreover, the insertion did not disrupt the reading frame between BCR and ABL and did not produce a premature stop codon. Instead, this novel BCR-ABL chimeric transcript encoded a functional oncoprotein with an in-frame insertion of 15 new amino acids.

Second case of CML with aberrant BCR-ABL fusion transcript (e8/a2) with insertion of an inverted ABL intron 1b sequence

We found a case of Ph-positive chronic myelogenous leukemia (CML) patient with an atypical BCR-ABL transcript that was undetectable by a routine reverse transcription polymerase chain reaction (RT-PCR) for major BCR-ABL. Additional RT-PCR and sequence analyses have demonstrated that the aberrant transcript consists of a fusion of BCR exon 8 (e8) and ABL exon 2 (a2) with an insertion of a 55-bp inverted sequence of intron 1b between them. The nucleotide sequences of the aberrant transcript were identical to those of a previously reported CML patient. These are the only two CML cases in the literature with identical aberrant BCR-ABL transcripts.