GSE173995
Efficient Elimination of Acute Myeloid Leukaemia Cells through Inhibition of KDM4A
We previously identified an essential role for the H3K9me3 histone demethylase, KDM4A, in maintaining AML cell survival, with genetic depletion by shRNA of KDM4A inducing leukaemic cell death with little effect on normal haematopoiesis. We hypothesised KDM4A inhibition may represent a novel and effective strategy to treat AML. To address this, we provided proof-of-principle for the use of KDM4 inhibitors (KDM4Ai) and fully characterised their functional potential in AML cells and identified the epigenetic mechanisms underpinning the essential role of KDM4A activity in THP-1 cells using both ChIP-seq and RNA-seq, delineating and functionally validating the epigenomic network regulated  by KDM4A, showing that selective loss of KDM4A is sufficient to induce apoptosis in a broad spectrum of human AML cells. This detrimental phenotype results from a global accumulation of H3K9me3 and H3K27me3 at KDM4A targeted genomic loci thereby causing down-regulation of a KDM4A-PAF1 controlled transcriptional program essential for leukemogenesis, distinct from that of KDM4C. Overall design: Preliminary data collection identified the best concentration and most appropriate timepoint for harvest of THP-1 cells treated with 30µM IOX1 (Tocris, #4464), 50µM IOX1, 100µM IOX1 alongside DMSO as a vehicle control in triplicate. Cells were grown in R10 with a final concentration of 0.1% vehicle across all samples. RNA-seq libraries were produced using the TruSeq stranded mRNA kit (Illumina) and single-end sequenced using the Illumina NextSeq 500 platform. For ChIP-seq, DNA was purified using Diagenode's iPure kit v2 and libraries made using the TruSeq ChIP Library Preparation Kit according to the manufacturer's instructions.