Imbalances of the 9q34 Region Downstream of ABL Gene in CML Are Associated with Blast Crisis.

Chronic myeloid leukaemia (CML) is a pluripotent haematopoietic stem cell disorder defined by expression of the BCR-ABL fusion gene, a constitutively activated tyrosine kinase. The fusion gene commonly results from formation of the Philadelphia chromosome after a t(9;22)(q34;q11) or related variant rearrangement. The disease follows a biphasic course with an initial benign chronic phase (CP) of 3–4 years treatable with agents such as Imatinib, followed by a rapidly fatal transformation resembling an acute leukaemia (blast crisis, BC). The CML blast crisis has been linked to a number of secondary chromosome changes leading to genome imbalances, such as additional Ph, +8, +9, iso17q. Prognostic scores based on clinical criteria (Sokal and Hasford scores) have been replaced with the discovery of other cytogenetic abnormalities occurring simultaneously at the time of translocation, such as deletions flanking the ABL/BCR breakpoint at the der(9)t(9;22) chromosome that lead to a significantly worse prognosis. We undertook array CGH analysis using an oligo based platform (Agilent) on 46 CML patients (25 CP, 19 BC & 8 in both phases) and 12 CML cell lines revealed a range of recurrent genomic imbalances. Two sets of recurrent cryptic imbalances were identified. These represented both gains and high-level amplifications affecting the 9q34.12 region immediately downstream of ABL gene, as well as losses or gains in the distal part of the 9q34-qter segment. These imbalances were found only in patients at the BC stage. Furthermore, in cases with follow-up samples, the 9q34 imbalances were present in the advanced stage of disease thus confirming their secondary nature. Among the genes found to be amplified in CML/BC is NUP-214, a nucleoporin gene, recently implicated in T-cell acute lymphoblastic leukaemia, thus suggesting an important role for cell clone survival. Confirmation of these amplifications was sought using fluorescent in situ hybridisation (FISH). A dual fusion probe targeting the ABL-NUP214 region was applied to a selection of twenty three patients with confirmed CML and features such as deletion of der(9) chromosome or resistance to treatment with Imatinib, shown to be more prone to variation within the CML phenotypeAmplification of the NUP214 region was found in five patients. These findings represent the first reports of NUP214 amplifications in CML, paving the way for future work.