Single cell analysis reveals mechanisms of heterogeneity and plasticity of leukemia initiating cells [CITEseq]

Leukemia initiating cells (LICs) self-renew indefinitely to fuel leukemic growth and spark disease relapse. Previously thought to be primitive and rare, the LIC state may actually be heterogeneous and dynamic, allowing LICs to evade therapy. Here, we use single cell transcriptomics to dissect the ontogeny of MLL-rearranged B-lymphoblastic leukemia (MLL-r B-ALL). Although we identify primitive, rare LICs, we also find more phenotypically differentiated LICs that possess the capability to replenish the full cellular diversity of MLL-r B-ALL. We find that activation of MYC-driven oxidative phosphorylation drives this process of cell state conversion, defining a new mechanism of LIC plasticity. This study was initially designed to define LICs in MLL-r B-ALL, relying on xenotransplantation with LDA and terminal leukemia incidence by day 150 post-transplant as endpoints. This endpoint was chosen based on the approximately 100-day latency of bulk transplanted leukemia cells at a dose of 10,000 cells per transplant. We hypothesized that transplantation of LIC-enriched populations would shift latency earlier and transplantation of LIC-depleted would shift the latency further. Leukemia populations were isolated and xenotransplanted with investigators monitoring recipient mouse health blinded to the cell source. At the onset of morbidity, mice were euthanized to harvest tissues and bone marrow. At the completion of the experiment, the experimental conditions were unblinded, and LIC frequency calculated by LDA analysis, or survival analyzed by log-rank test, where indicated. For quantification of flow cytometry or expression data, the statistical tests used are indicated. Student’s t-tests were used and analysis was unpaired, except where otherwise indicated. The raw data will be available at dbGaP. dbGap number: 42161 The study is called 'Study of leukemia stem cells in B-ALL' registered to Robert Rowe.