Pax5 haploinsufficiency cooperates with BCR-ABL1 to induce acute lymphoblastic leukemia

Acute lymphoblastic leukemia (ALL) is the commonest pediatric malignancy and comprises several distinct subtypes each with its own unique pathogenesis, clinical behavior, and response to therapy. Chromosomal aberrations are a hallmark of ALL but alone fail to induce leukemia. Pediatric ALLs can be divided into several categories based on the expression of several genetically conserved chromosomal translocations including the t(9,22)[BCR-ABL1], t(1,19)[TCF3-PBX1], t(12,21)[ETV6-RUNX1], MLL rearranged leukemia's, hyperdiploid and hypodiploid karyotypes, and T-lineage leukemia. Each translocation confers a characteristic transforming phenotype within the cell in which it originates but is alone insufficient to induce overt leukemia. In order to identify oncogenic lesions that cooperate with the aforementioned initiator lesions, we have performed genome-wide analysis of leukemia cells from 242 pediatric ALL patients using high resolution, single-nucleotide polymorphism microarrays.;The Philadelphia chromosome, a chromosomal abnormality that encodes BCR-ABL1, is the defining lesion of chronic myelogenous leukemia (CML) and a subset of ALL. To specifically define oncogenic lesions that cooperate with BCR-ABL1 to induce ALL, we subsequently performed genome-wide analysis of diagnostic leukemia samples from 304 individuals with ALL, including 43 BCR-ABL1 B-progenitor ALLs and 23 CMLcases. IKZF1 (encoding the transcription factor Ikaros) was deleted in 83.7% of BCR-ABL1 ALL, but not chronic-phase CML. Deletion of IKZF1 was also identified as an acquired lesion at the time of transformation of CML to ALL (lymphoid blast crisis). The IKZF1 deletions resulted in haploinsufficiency, expression of a dominant-negative Ikaros isoform, or the complete loss of Ikaros expression. Sequencing of IKZF1 deletion breakpoints suggested that aberrant RAG-mediated recombination is responsible for the deletions. These findings suggest that genetic lesions resulting in the loss of Ikaros function are an important event in the development of BCR-ABL1 ALL.;Secondary transplant studies confirmed that this was ALL and not a lymphoproliferative disorder. Immunophenotypic analysis confirmed the B-ALL phenotype and further revealed striking differences between Pax5+/+, Pax5+/-, and Pax5-/- leukemias. The leukemias that have lost either one or both Pax5 alleles revealed a more immature immunophenotype that was most pronounced in those with bi-allelic Pax5 loss. The wild-type leukemias were consistent with a Hardy fraction C immunophenotype while the Pax5 null leukemias were akin to Hardy fraction A with no expression of any definitive B-cell surface antigens except B220 and CD43.;The Pax5+/+ and Pax5 +/- leukemias were monoclonal while the Arf +/- and the compound heterozygous (Pax5+/- Arf+/-) leukemias were oligoclonal suggesting that the loss of p19Arf confers greater leukemogenic properties to a cell than does Pax5 loss. This is substantiated by the data that Arf heterozygous animals are tumor prone alone while Pax5 heterozygous animals live full normal lives.;Genomic analysis of 50 murine leukemias (15 WT, 25 Pax5 +/- and 10 Arf+/-) revealed that some of the same genomic abnormalities found in human ALL also develop in our murine ALL model. This finding suggests that our model is accurately recapitulating the development of human ALL. Furthermore, we have found through extensive gene expression studies that our mouse BCR-ABL1 leukemias share a gene expression profile similar to human BCR-ABL1 leukemias further supporting our murine model of ALL.;Recently D.J Wong et al performed an exhaustive study of embryonic and adult stem cell gene expression profiling. He found that there are modules of genes that are common to either embryonic or adult stem cells. He went further to delineate a group of genes that are commonly expressed in both murine and human embryonic stem cells and call this the core ESC-like module. We performed gene set enrichment analysis (GSEA) using this core ESC-like module and found that this geneset is significantly enriched in our murine leukemias. In addition, we found that this core ESC-like module was significantly enriched in normal Hardy fraction B cells, but not in A, or C-F. (Abstract shortened by UMI.)...