Genome wide analysis of Philadelphia positive (Ph+) acute lymphoblastic leukemia (ALL) reveals a recurring deletion of VPREB1 gene which affects B-cell differentiation

Background: ALL is a disease characterised by lack of differentiation and uncontrolled proliferation of lymphocyte precursor cells, driven by activation of oncogenes and inactivation of tumour suppressor genes. About 30% of B-cell ALL carries the Philadelphia chromosome (Ph), originated by the translocation t(9;22)(q34;q11), and thus express the fusion gene BCR-ABL. The constitutively active tyrosine kinase encoded by BCR-ABL blocks the differentiation of B precursor cells, prevents apoptosis and also causes genetic instability. This ultimately leads to the acquisition of new mutations, resistance to BCR-ABL inhibitors and disease progression. In particular BCR-ABL stimulates DNA repair by non-homologous end-joining and homologous recombination repair mechanisms after various genotoxic stimuli, but a lot of deletions and abnormalities are also generated. Methods and patients: In order to identify whether some genetic lesions could contribute to genetic instability in Ph+ ALL, we analyzed the genome of 18 Ph+ ALL patients using high-resolution single nucleotide polymorphism (SNP) array. 250 ng of genomic DNA were processed on 250K NspI array according to protocols provided by the manufacturer (Affymetrix Inc., Santa Clara, CA, USA). Copy number state was calculated with respect to a set of 48 Hapmap normal individuals using Partek® Genomics Suite. Fluorescence in situ hybridization (FISH) and real-time quantitative polymerase chain reaction (PCR) were performed to validate our results. Results: We found a significant deletion on chromosome 22, cytoband q11.22, close to immunoglobulin lambda light chain genes, in the region 20913571-20931814, corresponding to the VpreB1 (CD179a, Pre-B-Lymphocyte gene 1) gene in about 30% of newly diagnosed Ph+ ALL patients. It is highly conserved among mammals and selectively expressed during the pre-B stage of B cells ontogenesis and together with IGLL1 encodes for the surrogate light chain of the pre-B cell receptor. In mice its monoallelic deletion is associated with an increase of lymphocytes in pre-B stage in bone marrow, while its complete absence causes the impossibility to generate mature B cells. Since Ph+ ALL cells are immunophenotypically blocked at the pre-B stage, we are investigating whether VpreB1 deletion could interfere with normal B cell development and thus could have a role in leukeamogenesis and disease progression. Conclusion: This study demonstrated that the use of high-resolution SNP array is a powerful technology to detect genetic anomalies not revealed by classical cytogenetics which may provide new insights into leukemogenesis