Combined inhibition of transcription initiation and histone deacetylation triggers blood cancer cell death

Introduction: Blood cancer cells, including acute-myeloid-leukaemia (AML), exhibit exquisite dependency on the transcriptional and epigenetic networks that sustain oncogenic-transcriptomes, and are acutely sensitive to drugs targeting transcriptional and epigenetic regulators. While transcriptional cyclin-dependent-kinase (tCDK) and epigenetic inhibitors have shown promise in pre-clinical research, as single agents they have not been broadly successful in clinical trials, highlighting the need to investigate novel combination approaches. Methods: We employed a high-throughput bio-molecular approach (MAC-seq) to screen parallel cell viability and gene-expression responses of aggressive mixed-lineage-leukaemia-rearranged-AML (MLLr-AML) cells to diverse tCDK-epigenetic regulator inhibitor combinations (TRICs). Integrated analysis of RNA-seq data was performed to determine combination-specific transcriptional responses, and cell biological responses to putative synergistic combinations were profiled across AML, chronic-myeloid-leukaemia, and multiple myeloma models. Changes in the molecular landscape induced by synergistic drug-pairings will be by genome-wide (nascent)-RNA- and chromatin-immunoprecipitation-sequencing. New findings: Our bio-molecular screen identified multiple tCDK-epigenetic inhibitor pairs that synergistically reduced AML cell viability and exhibited amplified perturbation of gene-expression. The diversity of transcriptional profiles observed was predominantly associated with the different tCDK inhibitors (CDK7, 8, 9, 11, 12/13) rather than epigenetic disruptors, with CDK11 inhibition most strikingly associated with a unique transcriptional identity. Combined inhibition of the transcription-initiation checkpoint CDK7 and histone deacetylation (HDAC) exhibits robust synergistic induction of blood cancer cell death, with CRISPR-Cas9 gene-editing experiments revealing differential contributions of distinct HDACs to blood cancer cell responses to combined CDK7-HDAC inhibition. Conclusions: Our study supports the combination of tCDK and epigenetic inhibitors for treatment of aggressive blood cancers, identifying co-targeting of transcription-initiation and histone-deacetylation as a robust strategy to drive blood cancer cell death.