Cooperation between Mutant IL7R and TLX3 Generates Mixed Myeloid/Lymphoid Leukemia from Thymocyte Progenitors

Acute lymphoblastic leukemia (ALL) is the most common cancer in children. Despite current pediatric treatment protocols that have resulted in 5-year overall survival rates up to 90%, treatments have substantial side effects. Therefore, it is important to identify more specific therapeutic targets and develop more effective and less toxic drugs and drug combinations. We have shown that overexpression of TLX3 in association with mutant IL7R (mutIL7R) is sufficient to generate aggressive leukemia from transduced CD4-CD8- (DN) thymocyte progenitors. To better understand mutIL7R/TLX3-mouse leukemia, we combined single cell RNA sequencing (scRNAseq), Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), DNA Next Generation Sequencing (NGS) and flow cytometry to explore the cooperation of mutIL7R and TLX3 in orchestrating leukemogenesis. We found that mutIL-7R+TLX3 induced murine mixed T/myeloid leukemia. Myeloid cell clones (CD11b+) expressed identical TCR rearrangements with T cell clones (CD8+), indicating that mutant IL-7R+TLX3 generates mixed leukemia from T cell progenitors. Moreover, the passaged leukemia lost the T-cell phenotype and acquired a pro-B-like phenotype, suggesting preferential expansion of pro-B cells (CD19+, B220+ IgM-), which were not detected in the founder leukemia presumably due to its low frequency. We next sought to determine whether the oncogene combination is sufficient to drive a similar immunophenotype profile in vitro. We showed that ectopic expression of mutIL7R and TLX3 in DN primary thymocytes pushed the cells to myeloid (CD11b+, Gr1+) and B-cell (B220) phenotype over a time course of 4, 8 and 20 days, while T-cell development was blocked, suggesting that TLX3 expression prevented differentiation into CD4+/CD8+ T-cells. To further characterize the mixed T/myeloid leukemia at the molecular level, we compared the leukemia expressed genes to a TLX-bound genes public dataset. We found that 42 TLX3 target genes are expressed in mutIL7R+TLX3 leukemia. Interaction network analysis suggested significant Myc stimulation. We then confirmed Myc upregulation at the protein level in a thymocyte cell line, indicating that mutIL7R alone induces Myc but requires TLX-3 cooperation to induce maximal Myc expression levels. Taken together, we generated a high-resolution dataset with detailed information about the transcriptional landscape and immunophenotype of leukemia generated by mutIL-7R+TLX3, a combination that is observed in patient samples, and suggests new therapeutic drug strategies.