CDK7 Inhibition Targets Proliferative and Metabolic Oncogenic Vulnerabilities in Multiple Myeloma

Multiple myeloma (MM) cells are characterized by cell cycle dysregulation, epigenetic heterogeneity, and a perturbed transcriptional landscape. Given that CDK7 impacts RNA PolII transcriptional activity, the cell cycle, and the activity of most CDKs, it has emerged as a high-value therapeutic target. Indeed, inhibiting it with THZ1 potently reduces MM cell proliferation in vivo through the downregulation of MCL-1, BCL-XL, and c-MYC. However, THZ1 also equipotently targets CDK12 and CDK13, making the exact cellular phenotypes of CDK7 inhibition unknown.

To explore the molecular role and potential as a therapeutic target in MM, we targeted CDK7 via genetic perturbation, degradation and small molecule inhibition using the covalent inhibitor YKL-5-124, which elicited a strong therapeutic response in MM cells with minimal effects on normal cells. We observed that CDK7 inhibition was associated with a potent restoration in the Rb activity which plays a pivotal role as a tumor suppressor in the negative regulation of the cell cycle. This resulted in the selective downregulation of cell cycle control genes and the E2F-controlled program, which controls the cell cycle and DNA replication. To investigate whether Rb is the sole mediator of the effects of CDK7 inhibition, we ectopically expressed the T121 fragment of the SV40 large T antigen, which inactivates the three members of the Rb family. In MM cells, this partially overcame S phase arrest (from 8.5% to 30.4%) and growth inhibition (~2x) observed upon YKL-5-124 treatment and restored E2F1 chromatin binding.

Concordant with previous studies, CDK7 inhibition downregulated MYC-induced gene expression programs and MYC-associated biological modules. Importantly, the effects of CDK7 chemical inhibition were significantly reduced by inactivating MYC, as shown in P493-6 Burkitt’s lymphoma cells, which bear a Tet-repressible MYC construct. The essential role of CDK7 in sustaining MYC activity in MM cells was confirmed in vivo in a genetically engineered Vk*MYC mouse model. De novo mice had reduced amounts of monotypic serum immunoglobulins. In addition to downregulating MYC- and E2F-driven transcription, CDK7 inhibition caused a rapid decrease in MYC protein abundance and impaired the oncogenic MYC-regulated glycolytic cascade in MM. The resulting increase in reactive oxygen species and DNA damage is likely the mechanism for the observed tumor cell apoptosis caused by CDK7 inhibition in vitro and in vivo. Moreover, the inhibition of HK2 and lactate production by YKL-5-124 confers higher sensitivity to BRD4 inhibition and the anti-MM agents bortezomib and lenalidomide, even in resistant models.

These data show that, through its role as a critical cofactor and regulator of MYC and E2F activity, CDK7 is a master regulator of the oncogenic cell cycle, transcription, and metabolism in MM. CDK7 inhibition with YKL-5-124 represents an attractive and therapeutically actionable molecular vulnerability.