Differential activity of specific inhibitors of transcription regulating cyclin-dependent kinases in thyroid cancer cells.

'Superenhanced' transcription of oncogenes by aberrant looping of upstream enhancer elements to transcriptional regulatory regions is a mechanism of oncogene overexpression. Non-selective cyclin-dependent kinase inhibitors (CDKi) that target transcriptionally regulatory CDKs, including CDK7, 9, 12 and 13, reduce mRNA levels of super-enhanced oncogenes and have activity against thyroid cancer cells. We hypothesized that more specific inhibitors of CDKs would have differential activities in thyroid cancer cells and may be suitable for further studies. We selected thyroid cancer cell lines with a variety of genetic drivers for initial screening studies with CDK7/12/13 (THZ1) and CDK9 (AZD4573) inhibitors. IC50 values ranged from 5 to 100 nM for THZ1 for all cell lines and six of eight cell lines for AZD4573, with inhibition of RNAPII phosphorylation and evidence of reduced cell migration. Four thyroid cancer cell lines with common driver mutations, including 8505C (BRAFV600E), BCPAP (BRAFV600E), TPC1 (RET fusion) and FTC133 (PTEN null), were selected for detailed studies with more specific inhibitors. In these cells, the CDK 12/13 inhibitor (SR-4835) and AZD4573 were more effective than the specific CDK7 inhibitor YKL-5-124 at reducing cell survival, migration and proliferation, and at inducing apoptosis. Treatment with SR-4835 was the most potent, induced DNA damage and resulted in cyclin K loss. Combined reduction in CDK12/13 levels with siRNA reduced RNAPII phosphorylation. These data suggest that specific inhibitors of CDK12/13 may be particularly active in thyroid cancer cell lines; further studies evaluating their efficacy are warranted in thyroid cancer.