CDK12 is hyperactivated and a synthetic-lethal target in BRAF-mutated melanoma

Abstract

Melanoma is the deadliest form of skin cancer and considered intrinsically resistant to chemotherapy. Nearly all melanomas harbor mutations that activate the RAS/mitogen-activated protein kinase (MAPK) pathway, which contributes to drug resistance via poorly described mechanisms. Herein we show that the RAS/MAPK pathway regulates the activity of cyclin-dependent kinase 12 (CDK12), which is a transcriptional CDK required for genomic stability. We find that melanoma cells harbor constitutively high CDK12 activity, and that its inhibition decreases the expression of long genes containing multiple exons, including many genes involved in DNA repair. Conversely, our results show that CDK12 inhibition promotes the expression of short genes with few exons, including many growth-promoting genes regulated by the AP-1 and NF-κB transcription factors. Inhibition of these pathways strongly synergize with CDK12 inhibitors to suppress melanoma growth, suggesting promising drug combinations for more effective melanoma treatment.

The CDK12 inhibitor SR-4835 functions as a molecular glue that promotes cyclin K degradation in melanoma

“…cells were recently shown to display high CDK12 activity 13 . To assess its role in these cells, we treated five BRAF-mutated melanoma cell lines (Colo829, A375, WM164, WM983A, WM983B) with increasing concentrations of SR-4835, a recently described ATP-competitive inhibitor of CDK12 and CDK13 16 .…”

“…These experiments characterized the molecular glue activity of SR-4835 analogs, and confirmed the role played by the benzimidazole side-chain for cyclin K degradation. 8,23 , including melanoma 13 , making it an attractive therapeutic target. To characterize the mechanism of action of SR-4835, a recently described CDK12 inhibitor 16 , we performed a genome-wide CRISPR/Cas9 loss-offunction screen in A375 melanoma cells.…”

“…In HER2positive breast cancer, CDK12 was shown to be co-amplified with the HER2 oncogene, and to promote migration and invasion of HER2-positive breast tumor cells 10 . CDK12 plays an important role in the growth of cancers driven by dysregulated transcription factors, such as MYC (neuroblastoma) 11 and the EWS-FLI1 fusion (Ewing sarcoma) 12 , or in melanoma driven by activating mutations in BRAF 13 . In other cancers, including ovarian 14 , prostate 15 , and breast 16 , loss of CDK12 leads to the downregulation of DDR genes, which increases genomic instability and sensitivity to chemotherapy.…”

“…At high concentrations, THZ1 can also inhibit CDK12, which was exploited in the design of THZ531 18 . THZ531 inhibits both CDK12 and CDK13, and studies have shown that THZ531 reduces Pol II phosphorylation and the proliferation of many types of cancer cells 12,13,18,19 4835 is another highly selective CDK12/13 inhibitor that act as an ATP antagonist 16 . SR-4835 was shown to reduce Pol II phosphorylation and to induce rapid tumor regression in multiple mouse models 16 .…”

Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release

“…In addition, CDK12 can act as a facilitator or an effector of oncogenic signaling pathways. While CDK12 facilitates activation of ERBB–PI3K– AKT and WNT signaling pathways in HER2 -positive breast cancer through promoting transcription of an RTK adaptor IRS-1 and WNT ligands genes, respectively (31), it is constitutively activated by the hyperactive RAS–BRAF–MEK1/2–ERK1/2 signaling pathway in BRAF-mutated melanoma (32).…”