Novel inhibition of transcriptional cyclin-dependent kinases, CDK12/13, using CT7439 as a treatment for colorectal cancer with CDK12 upregulation

Introduction: Cell proliferation is a hallmark of cancer growth, and regulation of transcription and translation is key to controlling proliferative capacity. A crucial connection between transcriptional regulation and the cell cycle occurs via transcriptional cyclin-dependent kinases (CDKs), CDK12 and its paralog, CDK13, which regulate transcription by phosphorylating the c-terminal domain of RNA polymerase II. Both CDK12 and CDK13 are often upregulated in solid tumors, rendering them compelling targets for therapeutic intervention. Methods: A total of eight CDK12 or CDK12/13 inhibitors with different mechanisms of action (covalent, non-covalent, proteolysis-targeting chimera, and molecular glue) were screened against a panel of cancer cell lines spanning five solid tumor types (breast, colorectal, lung, ovarian, and prostate). Colorectal cancer patient-derived organoids (PDO) were used to validate the most efficacious agents, covalent binders (THZ531 and CDK12-IN-E9). In order to determine whether CDK13 plays a compensatory role for loss of CDK12 function, knockdown of CDK13 by siRNAs was employed, followed by CDK12-specific inhibition using a proteolysis-targeting chimera (BSJ-4-116). Finally, synergy was conducted to determine whether CDK12/13 inhibition increases sensitivity to poly-ADP ribose polymerase (PARP) inhibition. qPCR quantified the presence of short and long isoforms of BRCA1 following CDK12/13 inhibition to confirm whether transcription elongation in DNA damage repair genes was prevented. Results: Covalent inhibition of CDK12/13 was the most efficacious across pan-cancer cell lines. Validation in colorectal cancer PDO showed greater inhibition by covalent inhibitors than standard of care chemotherapies for colorectal cancer (oxaliplatin, SN38, and 5-FU). CDK13 siRNA-mediated knockdown sensitized colorectal cell lines to the CDK12-specific inhibitor, BSJ-4-116, suggesting CDK13 may compensate for CDK12 loss of function. CDK12/13 inhibition led to downregulation of long isoforms of BRCA1, rendering cells susceptible to dual CDK12 and PARP inhibitors. These compelling data prompted evaluation of CT7439, a CDK12/13 inhibitor and cyclin K glue-degrader, which showed efficacy in the low nanomolar range for a panel of colorectal PDO. Conclusions: Here we highlight CDK12/13 inhibition as a compelling target for colorectal cancers and other solid tumors and show the importance of CDK13 compensation during CDK12 inhibition. These findings support further evaluation of the novel CDK12/13 inhibitor, CT7439, for the treatment of solid tumors with CDK12/13 upregulation.