Localization of preferential sites of rearrangement within the BCR gene in Philadelphia chromosome-positive acute lymphoblastic leukemia.

Abstract

The Philadelphia chromosome associated with acute lymphoblastic leukemia (ALL) has been linked to a hybrid BCR/ABL protein product that differs from that found in chronic myelogenous leukemia. This implies that the molecular structures of the two chromosomal translocations also differ. Localization of translocation breakpoints in Philadelphia chromosome-positive ALL has been impeded due to the only partial characterization of the BCR locus. We have isolated the entire 130-kilobase BCR genomic locus from a human cosmid library. A series of five single-copy genomic probes from the 70-kilobase first intron of BCR were used to localize rearrangements in 8 of 10 Philadelphia chromosomepositive ALLs. We have demonstrated that these breakpoints are all located at the 3' end of the intron around an unusual restriction fragment length polymorphism caused by deletion of a 1-kilobase fragment containing Alu family reiterated sequences. This clustering is unexpected in light of previous theories of rearrangement in Philadelphia chromosomepositive chronic myelogenous leukemia that would have predicted a random dispersion of breakpoints in the first intron in Philadelphia chromosome-positive ALL. The proximity of the translocation breakpoints to this constitutive deletion may indicate shared mechanisms of rearrangement or that such polymorphisms mark areas of the genome prone to recombination.Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy afflicting 1 in 30,000 children annually (1). Though therapeutic advances have resulted in long-term disease-free survival rates of 60% (2), those tumors that contain a karyotypic abnormality have a significantly poorer prognosis (3). This would suggest that neoplastic mechanisms may be at work as a consequence of chromosomal rearrangement that make these tumors more resistant to treatment. The most common karyotypic abnormality seen in ALL is the Philadelphia chromosome (Ph). It is this same chromosomal translocation that is characteristically linked to >90% of patients with chronic myelogenous leukemia (CML) (4). In ALL, however, the Ph is less frequently observed and is present in =10% of patients (5). Karyotypic analysis has revealed that this marker chromosome is a result of a reciprocal translocation between chromosome 9 band q34 and chromosome 22 band qll.2: t(9;22)(q34;qll.2) (6).Though these rearrangements in ALL and CML are karyotypically indistinguishable, their molecular structures differ. In both instances this translocation results in the juxtaposition of upstream regions of the BCR gene located on chromosome 22 to a distal portion of the ABL protooncogene on chromosome 9 (7-10). This results in the formation of both hybrid BCR/ABL transcripts and proteins (11,12). In CML, this rearrangement has been mapped to within a 5-to 6-kilobase pair (kb) BCR (23,24). Breakpoint locations of the majority of Ph' ALL have eluded molecular definition. Since only portions of the large first intron have been isolated, it has been postulated that these mol...

Characterization of the translocation breakpoint sequences in philadelphia‐positive acute lymphoblastic leukemia

“…For example, ALU sequences are found in some cases only in the chromosome 9 breakpoint region (i.e., FY and SUP-B13). From our sequence data (van der Feltz et al, 1989;this study, and Papadopoulos, Kabarowski, and van der Feltz, unpublished data) as well as that of Denny et al (1989), we can determine that no ALU sequence is present for at least 800 bases upstream of the FY breakpoint on chromosome 22 (in a deleted allele) and the closest ALU sequence to the SUP-B13 breakpoint is that present in the deletion polymorphism more than 1.1 kb upstream. In addition, since the FY2 (van der Feltz et al, 1988) and 2.3 EB/9q+ (Rubin et al, 1988b) can be used as unique probes, we can infer that no conserved ALU repeat family members reside in the 1.95 kb 3' of the SUP-B13 breakpoint and 2.7 kb region 3' of the FY breakpoint.…”

Characterization of the BCR promoter in Philadelphia chromosome-positive and -negative cell lines.

“…This results in hybrid BCR-ABL transcripts and proteins (9,11,12,31,46). Though c-ABL breakpoints are scattered throughout the large first intron of c-ABL in both Ph+ ALL and CML, the sites of BCR rearrangement differ (10,17,25). These differences reflect the amount of BCR sequences incorporated into the BCR-ABL product.…”

BCR first exon sequences specifically activate the BCR/ABL tyrosine kinase oncogene of Philadelphia chromosome-positive human leukemias.

“…The breakpoints for the gene encoding P210 fall within the introns of a 5.8-kb region spanning a cluster of five small BCR exons (14). The breakpoints for the gene encoding P185 predominantly fall within a 20-kb region at the 3' end of the 70-kb first intron of BCR (3,8). The two chimeric BCR/ABL proteins induce transformation of lymphoid cells in vitro (33,34) and produce lymphoid and myeloid leukemias in mice (7,10,18,23).…”