The novel BETi BI 894999 represses super-enhancer associated transcription and synergizes with CDK9 inhibition in AML by induction of apoptosis

Bromodomain and extra-terminal (BET) protein inhibitors have been reported as treatment options for acute myeloid leukemia (AML) in preclinical models and are currently being evaluated in clinical trials. This work presents a novel potent and selective BET inhibitor (BI 894999), which has recently entered clinical trials (NCT02516553). In preclinical studies, this compound is highly active in AML cell lines, primary patient samples, and xenografts. HEXIM1 is described as an excellent pharmacodynamic biomarker for target engagement in tumors as well as in blood. Mechanistic studies show that BI 894999 targets super-enhancer-regulated oncogenes and other lineage-specific factors, which are involved in the maintenance of the disease state. BI 894999 is active as monotherapy in AML xenografts, and in addition leads to strongly enhanced antitumor effects in combination with CDK9 inhibitors. This treatment combination results in a marked decrease of global p-Ser2 RNA polymerase II levels and leads to rapid induction of apoptosis in vitro and in vivo. Together, these data provide a strong rationale for the clinical evaluation of BI 894999 in AML. Overall design: We performed ChIP-seq experiments in 22 samples covering 4 different cell lines and 3 different antibodies (H3K27ac, BRD4, RNA Pol-II). Some experiments were performed using 2 biological replicates. Technical replicates (if available) were merge in the respective FASTQ files. All published ChIP-seq results were derived from merged biological replicates for the specific ChIP-seq experiment with respect to the cell line specific input. Unique numbers in the sample/result names assign the FASTQ files to their processed output files. We also performed Quant-seq in-vivo experiments in 27 cell-line derived xenografts (MV-4-11-B) using 3-4 replicates. Control samples are detonated as the Natrosol treated samples. Lastly, we performed RNA-seq experiments in 38 samples covering 6 different cell lines. These experiments were performed using 2 biological replicates. Note, the compound mentioned in the paper LDC000067 is identical to EX00101218 - these are two different identifiers for the same molecule.