Identification of the deleted gene(s) associated with the Philadelphia rearrangement responsible for poor outcome in ∼20% of patients with CML

Using fluorescence in situ hybridization (FISH) we found that a significant percentage of CML patients with a poor clinical response have submicroscopic deletions resulting in loss of sequences adjacent to the ABL and BCR on the derivative chromosome 9, suggesting that the presence of genomic deletions in the vicinity of the ABL/BCR gene on der(9q) have prognostic significance. Similar deletions, adjacent to the breakpoints, were identified in other recurrent chromosomal rearrangements of leukemia. Analysis of sequence data from the each of breakpoint regions suggested that submicroscopic deletions occur in regions with a high density of Alu repeats. We then used real time quantitative (Q-PCR) analysis to determine the frequency of more localized hemizygous genomic deletions in the region of the ABL/BCR gene associated with poor outcome in CML and to map the minimal deleted region (MDR) critical for adverse outcome. We have identified an additional 10–15% of CML patients with hemizygous deletions in the region of the ABL/BCR fusion gene that would not have readily been detected by conventional FISH methods. Our data defined for the first time the MDR on the der(9), extended for about 120 kb 5 ′ of the ABL gene but excluded all sequences telomeric of the BCR gene on chromosome 22. The MDR included the PRDM12 gene, that is predicted to function as a tumor suppressor gene, and its haploinsufficiency could promote oncogenesis, and affect outcome in CML. Our mapping of PRDM12 within the MDR on der(9) strongly suggests that PRDM12 is a specific target of deletions associated with the Philadelphia translocation. We have also evaluated the deletion status of CML patients receiving ST1571 using Q-PCR. Our study demonstrated a strong association between the presence of deletions in the ABL/BCR region and poor cytogenetic response to ST1571. Despite extensive research and knowledge in the area of CML there is still no reliable predictor of clinical outcome and treatment response. We propose that the presence of deletions in the 5′ ABL region of CML patients at diagnosis can serve as a new valuable prognostic marker that can be used in guiding the management of CML patients.