Investigating the Role of ZNF384 Rearrangements in Acute Leukemia

"Chromosomal rearrangements involving ZNF384 are the defining lesion in 5% of pediatric and adult B-cell acute lymphoblastic leukemia and tumors are characterized by aberrant myeloid marker expression. Additionally, ZNF384 rearrangements are the defining lesion in nearly half of pediatric B/myeloid mixed phenotype acute leukemia. These fusions juxtapose full-length ZNF384 to the N terminal portion of a diverse range of partners, most often, transcription factors or epigenetic modifiers. It has been shown that ZNF384-rearranged tumors have a distinct gene expression profile that is consistent between disease groups and N terminal partners. Genomic analyses of patient tumors has shown that ZNF384 fusions arise in hematopoietic stem cells and that expression of the fusion, but not the concomitant genetic alterations, results in lineage aberrancy, however, the mechanistic role of ZNF384 rearrangements has not been formally studied. The goal of this project was to investigate the role of ZNF384 rearrangements, together with concomitant genetic alterations, in leukemogenesis, with an emphasis on characterizing the role of cell-of-origin and lineage of the resulting leukemias. Additionally, I aimed to explore the mechanism that leads to a distinct gene expression profile and immunophenotype. Using viral overexpression and newly developed genetically engineered mouse models I have shown the effect of ZNF384 fusion expression at multiple stages of hematopoietic development in mouse and human systems. These experiments revealed the hematopoietic skewing toward immature, myeloid differentiation caused by expression of ZNF384 fusions. While expression of ZNF384 fusion oncoproteins in either mouse or human hematopoietic progenitors resulted in hematopoietic expansion, lineage skewing, and for some fusion partners, self-renewal in vitro; co-expression with common concomitant lesions, such as NRAS G12D, was necessary in order to develop a fully penetrant mouse leukemia in vivo. In contrast, ZNF384 fusions alone drive B/myeloid leukemia when expressed in human hematopoietic stem and progenitor cells and transplanted into NSG-SGM3 mice, highlighting the benefits of using human models to investigate human oncogenes. Importantly, these experiments confirm that hematopoietic stem cells are the most sensitive to cellular transformation by ZNF384 fusions. Mechanistic studies integrating gene expression and chromatin occupancy data revealed that fusions bind canonical ZNF384 sites with greater intensity than wild type protein. A subset of regions with increased fusion binding also had increased H3K27Ac and were intronic or intergenic suggesting they are putative enhancer regions. These findings support that ZNF384 fusions occur in an early hematopoietic stem or progenitor cell which leads to skewed hematopoiesis and leukemic transformation in the presence of additional lesions, proliferative stress, or cytokine stimulation. This is likely caused by inappropriate extended activation of stem and progenitor enhancer regions along with deregulation of lineage-specific genes by altered binding of ZNF384 fusions. Together, these results demonstrate an intersection of cell of origin and expression of fusion oncoproteins as necessary prerequisites for generating lineage ambiguous leukemia."