Novel and highly selective CDK9 inhibitors suppress proliferation of triple negative breast cancer (TNBC) cells in vitro

This study evaluates the efficacy of two newly developed selective CDK9 inhibitors (CDK9i) across a panel of TNBC cell lines. MDA-MB-453, MFM-223, MDA-MB-468 and MDA-MB-231 TNBC cells were treated with increasing concentrations of two novel and highly selective CDK9 inhibitors and the effect on proliferation, apoptosis and expression of CDK9 targets determined. MDA-MB-453 and -468 cells showed significant growth inhibition with as little as 150nM of CDK9i, evident 3 days after commencement of treatment. Both MDA-MB-231 and MFM-223 cells were less sensitive to the CDK9 inhibitors, with MDA-231 cells requiring at least 300nM to suppress growth. MFM-223 cells did not demonstrate any growth inhibition after 7 days of culture with CDK9i concentrations up to 1.2uM. Protein expression of CDK9 targets, including RNA Polymerase II (RNAPII), phosphorylated-RNAPII, the proto-oncogene C-MYC, and apoptotic marker cleaved caspase-3, were examined by Western blot after optimal CDK9i exposure across each cell line. CDK9i suppressed phosphorylated-RNAPII, but not total RNAPII, indicative of targeted CDK9 inhibition. The master transcription factor C-MYC, which is highly expressed in TNBC, was downregulated, and cleaved-caspase-3 was upregulated with CDK9i treatment. These data demonstrate cell specific efficacy of novel CDK9 inhibitors in cell line models of TNBC via transcriptional suppression of proto-oncogenes and upregulation of apoptotic pathways. Future studies will identify molecular markers of response to CDK9 inhibition and evaluate these novel inhibitors in TNBC patient derived xenografts.