IKZF1 (IKAROS) DELETIONS IN BCR-ABL1 POSITIVE ACUTE LYMPHOBLASTIC LEUKEMIA ARE ASSOCIATED WITH AN IMPAIRED B-CELL DIFFERENTIATION AND POOR OUTCOME

Introduction. The BCR-ABL1 fusion gene defines the subgroup of acute lymphoblastic leukaemia (ALL) with the worst clinical prognosis. Aim and Methods. To identify oncogenic lesions that combine with BCRABL1 to cause ALL, we used Affymetrix Genome-Wide Human SNP arrays (250K NspI and SNP 6.0) and genomic PCR to study 106 cases of adult BCR-ABL1-positive ALL. Results. The most frequent somatic copy number alteration was a deletion on 7p12 of IKZF1, which encodes the transcription factor Ikaros and was identified in 80 of 106 patients (75%). Two major deletions occurred: the first one (D4-7) was characterised by a loss of exons 4 through 7 (44/106, 42%), and the second one (D2-7) that we cloned was characterised by removal of exons 2 through 7 (20/106, 19%). A variable number of nucleotides (patient-specific) were inserted at the conjunction and maintained with fidelity at the time of relapse. The extent of the D4-7 deletion correlated with the expression of a dominant-negative isoform with cytoplasmic localisation and oncogenic activity, while the D2-7 deletion resulted in a transcript lacking the translation start site. The IKZF1 deletion was also identified in the progression of chronic myeloid leukaemia (CML) to lymphoid blast crisis (66%), but never in myeloid blast crisis or chronic phase CML, or in acute myeloid leukaemia patients. Known DNA sequence and structural features were mapped along the breakpoint cluster regions including heptamer recombination signal sequences (RSS) recognised by RAG enzymes during V(D)J recombination, suggesting that IKZF1 deletions could arise from aberrant RAG-mediated recombination. Using gene-set enrichment analysis to compare the gene-expression signatures of patients with IKZF1 deletion versus not-deleted patients, we identified a unique signatures characterized by down-regulation of genes involved in pre-B-cell differentiation (e.g. VPREB1, VPREB3, IGLL3, BLK) and upregulation of genes involved in cell-cycle progression (STK17B, SERPINB9, CDKN1A). These findings suggest that genetic alterations of IKZF1 influence the transcriptome and contribute to an impaired B-cell differentiation. We next investigated whether the IKZF1 deletions associated with a poor outcome. Univariate analysis showed that the IKZF1 deletion is a negative prognostic marker influencing the cumulative incidence of relapse (10.1 months for pts with deletion vs 56.1 months for wild-type pts, p=0.0103) and disease-free survival (DFS) (10.1 months vs 32.1 months, respectively, p=0.0229). The negative prognostic impact of the IKZF1 deletion on DFS was also confirmed by multivariate analysis (p=0.0445). Conclusions. Deletion of IKZF1 is an important event in the development of BCR-ABL1 B-progenitor ALL which significantly influences clinical outcome. It is likely that Ikaros loss combines with BCRABL1 to induce lymphoblastic leukaemia, arresting B-lymphoid maturation. Supported by: European LeukemiaNet, AIL, AIRC, FIRB 2006, Strategico di Ateneo, GIMEMA Onlus, Fondazione del Monte di Bologna e Ravenna, PIO project 2007.