SRA

Disruption of epigenetic regulation is a hallmark of Acute Myeloid Leukemia (AML), but therapeutic interventions are difficult by the interplay of epigenetic mechanisms controlling genomic elements. We hypothesized that concurrent targeting of aberrant promoter and enhancer epigenetic silencing improves efficacy against AML. To test this, we developed an ex vivo culturing system and treated 52 patient-derived AML with low-dose 5-Azacytidine and specific LSD1 inhibitors. Genetic analysis revealed that combination of 5-Azacytidine and LSD1 inhibition was most effective in TET2mut AML. Combination therapy further up-regulated expression of genes associated with both LSD1-bound enhancers and cytosine methylated promoters. Functional validation studies suggest that expression of these genes (e.g. GATA2, GFI1 and DLX2) contribute to drug efficacy. Mechanistically, combination therapy increased enhancer-promoter looping and chromatin-activating marks at the GATA2 locus. This gene induction effect was dampened by CRISPRi of the LSD1-bound enhancer in TET2mut AML. Concordant with TET2mut AML, knockdown of TET2 in human hematopoietic stem and progenitor cells induced loss of enhancer 5-hydroxymethylation and facilitated LSD1-mediated enhancer inactivation. Collectively, our platform revealed increased LSD1-mediated enhancer inactivation after TET2 deficiency that provided a basis for combinatorial epigenetic therapy to activate promoter-enhancer interactions. Overall design: ERRBS, ChIPseq and RNAseq profiles in AML ex vivo cultures treated with 5-Azacitidine and LSD1 inhibitor