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Cyclin-dependent kinase 9 (CDK9), a key regulator of RNA-polymerase II, is a candidate drug target for cancers driven by transcriptional deregulation. Here we report a multi-omics-profiling of prostate cancer cell responses to CDK9 inhibition to identify synthetic lethal interactions. These interactions were validated using live-cell imaging, mitochondrial flux-, viability- and cell death activation assays. We show that CDK9 inhibition induces acute metabolic stress in prostate cancer cells. This is manifested by a drastic down-regulation of mitochondrial oxidative phosphorylation, ATP depletion and induction of a rapid and sustained phosphorylation of AMP-activated protein kinase (AMPK), the key sensor of cellular energy homeostasis. We used metabolomics to demonstrate that inhibition of CDK9 leads to accumulation of acyl-carnitines, metabolic intermediates in fatty acid oxidation (FAO). Acyl-carnitines are produced by carnitine palmitoyltransferase enzymes 1 and 2 (CPT), and we used both genetic and pharmacological tools to show that inhibition of CPT-activity is synthetically lethal with CDK9 inhibition. To our knowledge this is the first report to show that CDK9 inhibition dramatically alters cancer cell metabolism.

Original publication

DOI

10.1016/j.neo.2019.05.001

Type

Journal article

Journal

Neoplasia

Publication Date

07/2019

Volume

21

Pages

713 - 720

Keywords

Apoptosis, Carnitine O-Palmitoyltransferase, Cell Line, Tumor, Cell Proliferation, Cyclin-Dependent Kinase 9, Fatty Acids, Humans, Male, Oxidation-Reduction, Oxidative Phosphorylation, Phosphorylation, Prostate, Prostatic Neoplasms, Signal Transduction