CDK7 inhibition suppresses aberrant hedgehog pathway and overcomes resistance to smoothened antagonists

Significance There have been FDA-approved anti-hedgehog drugs for treating hedgehog-driven cancers, which act by antagonizing the upstream component smoothened; however, resistance to smoothened inhibitor (SMOi) drugs have been described. Our previous study demonstrates that epigenetic or transcriptional targeted therapy represents an anti-hedgehog therapeutic strategy that can effectively overcome SMOi resistance. Here we report that transcriptional inhibition through targeting CDK7 suppresses the aberrant hedgehog pathway and growth of hedgehog-driven cancers either responsive or resistant to SMOi drugs, supporting CDK7 inhibition as a promising therapeutic strategy for overcoming SMOi resistance. Since multiple CDK7-targeted drugs have recently entered phase I trial for tumor therapy, our study provides the preclinical rationale for enrolling hedgehog-driven cancers into those clinical trials in the near future. The aberrant hedgehog (Hh) pathway plays important roles in multiple cancer types, therefore serving as a promising drug target. Current clinically available hedgehog-targeted drugs act mostly by antagonizing the upstream component smoothened; however, both primary and acquired resistance to FDA-approved smoothened inhibitor (SMOi) drugs have been described. We have recently demonstrated that the BET inhibitor effectively suppresses SMOi-resistant Hh-driven cancers through antagonizing transcription of GLI1 and GLI2, the core transcriptional factors of Hh pathway, suggesting epigenetic or transcriptional targeted therapy represents an anti-Hh therapeutic strategy that can overcome SMOi resistance. Here we performed an unbiased screening of epigenetic or transcriptional targeted small molecules to test their inhibitory effects on GLI1 and GLI2 transcription or cell viability of Hh-driven tumor lines. THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7), is identified as the top hit in our screening. We then confirmed that antagonizing CDK7 by either small-molecule inhibitors or the CRISPR-Cas9 approach causes substantial suppression of GLI1 and GLI2 transcription, resulting in effective inhibition of Hh-driven cancers in vitro and in vivo. More importantly, antagonizing CDK7 retains inhibitory activity against Hh-driven cancers with almost all so-far described primary or acquired SMOi resistance. Furthermore, we reveal a synergy between CDK7 inhibition and BET inhibition on antagonizing aberrant Hh pathway and Hh-driven cancers that are either responsive or resistant to SMOi. Our results illustrate transcriptional inhibition through targeting CDK7 as a promising therapeutic strategy for treating Hh-driven cancers, especially those with primary or acquired resistance to SMOi drugs.