Poster Presentation 40th Annual Lorne Genome Conference 2019

Genome-wide CRISPR screening reveals loss of STAGA complex activity mediates resistance to CDK7 inhibition   (#259)

Izabela Todorovski 1 2 , Stephin J Vervoort 1 , Ricky W Johnstone 1 2
  1. Peter MacCallum Cancer Centre, Bundoora, VIC, Australia
  2. Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia

Deregulated transcription is a hallmark of cancer and can arise from genetic alterations that modulate the activity of RNA Polymerase II (POL II)1. In recent years, direct targeting of core transcription components to disrupt oncogenic gene expression has proven effective in numerous malignancies.

A basal regulator of POL II necessary for the initiation of transcription, cyclin dependant kinase 7 (CDK7) has shown promise as a therapeutic candidate in pre-clinical cancer models2-5. Furthermore, malignancies with aberrant transcription programs driven by oncogenic fusion proteins, such as mixed lineage leukemia fusion protein (MLL-FP), and the MYC oncogene, are particularly sensitive to small molecule inhibition of CDK74-6.

Despite the therapeutic potential of CDK7 inhibitors (CDK7i), previous clinical experience using small molecule kinase inhibitors has illustrated the potential negative impact of primary and/or acquired resistance to these agents. As such, an understanding of how resistance to CDK7i may occur is necessary to ensure the success of these compounds in the clinic.

As a strategy to interrogate mechanisms of resistance to CDK7 targeting in a transcriptionally deregulated context, we transduced a human MLL-driven leukaemia cell line, stably expressing the Cas9 nuclease, with the Brunello and Gecko V2 genome wide CRISPR libraries. Following successive rounds of exposure to CDK7i, resistant cells were harvested and subject to next generation sequencing. Single guide RNAs that consistently and positively enriched in multiple screens using different CDK7i targeted the core module of the histone acetyltransferase and de-ubiquitnase SPT3-TAF9-GCN5 acetylase (STAGA) complex, previously shown to be a cofactor required for global POL II mediated transcription in budding yeast7,8.

These genome wide genetic screens demonstrate that the loss of STAGA complex components can mediate resistance to CDK7 inhibition, providing an opportunity for novel combinatorial therapeutic approaches. Moreover, this study offers novel insight into the regulation of transcription by POL II.

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