Targeting histone methylation to reprogram the transcriptional state that drives survival of drug-tolerant myeloid leukemia persisters

Although chemotherapy induces complete remission in the majority of acute myeloid leukemia (AML) patients, many face a relapse. This relapse is caused by survival of chemotherapy-resistant leukemia (stem) cells, called measurable residual disease (MRD). Here, we demonstrate that the anthracycline doxorubicin epigenetically reprograms leukemia cells by inducing tri-methylation of histone 3 lysine 27 (H3K27) and H3K4. Moreover, within a doxorubicin-sensitive leukemia cell population, we identified a subpopulation of reversible anthracycline-tolerant cells (ATCs) with leukemic stem cell (LSC) features lacking upregulation of doxorubicin-induced H3K27me3 or H3K4me3. These ATCs have a distinct transcriptional landscape than the leukemia bulk and could be eradicated by inhibition of KDM6. In primary AML, reprogramming the transcriptional state by targeting KDM6 reduced MRD load and survival of LSCs residing within MRD, and enhanced the response to chemotherapy in vivo. Together, our results reveal plasticity of anthracycline resistance in AML cells and highlight the potential of transcriptional reprogramming by epigenetic-based therapeutics to target chemotherapy-resistant AML cells. Overall design: K562 cells were seeded in 480 wells with 10.000 cells/well and treated with an increasing concentration of doxorubicin (up to 225 ng/ml). After 4 weeks, cells in 21 wells survived chemotherapy treatment. Cells from 4 wells could be maintained in culture in the presence of 225 ng/ul doxorubicin (ATC#1-4). To elucidate the transcriptomic state and regulatory circuits involved in the drug-tolerant condition of the persisters, we performed gene expression profiling analysis of RNA sequencing data for the sensitive K562 parental cells, parental cells shortly treated (48 hours) with 225 ng/ml doxorubicin, and ATC#1-4.