Genome-wide functional CRISPR screen reveals CDK7 as a targetable therapeutic vulnerability for head and neck cancer

Abstract

Background: Head and neck squamous cell carcinoma (HNSCC) remains a challenging prevalent lethal malignancy, with still scarce targeted therapies and rather limited clinical benefit. We conducted an optimized genome-wide functional CRISPR screen aimed at identifying actionable genetic vulnerabilities for rapid preclinical evaluation as novel targeted therapies. Cyclin-dependent kinases (CDKs) were prioritized as pivotal in cancer therapy. Methods: Whole-genome CRISPR KO screen was performed in a panel of five HNSCC cell lines. CDK7 was selected for further functional and molecular characterization. The effects of CRISPR CDK7 knockout (KO) and CDK7-selective inhibitors were thoroughly investigated in cellular models using viability, colony formation and apoptosis assays, cell cycle analysis, and global transcriptomics by RNAseq. CDK7 inhibition was also therapeutically evaluated in mouse xenografts and patient-derived organoids (PDOs). Results: CDK7 was identified as an essential gene across all five HNSCC cell lines screened. Genetic and pharmacological CDK7 inhibition significantly and consistently reduced tumor cell proliferation due to generalized cell cycle arrest and apoptosis induction. CDK7 KO, YKL-5-124 and samuraciclib also showed a potent antitumor activity effectively abrogating tumor growth in HNSCC PDOs and also in mouse xenograft models without significant toxicity. Mechanistically, CDK7 inhibition led to a broad downregulation of gene sets for cell cycle progression, DNA repair, and massively reduced the transcription of several essential genes and untargetable vulnerabilities identified by our CRISPR screen. Conclusions: CDK7 emerges as a promising targetable therapeutic vulnerability for HNSCC. Our study provides broad-based evidence for the robust antitumor activity of CDK7-selective inhibitors in disease-relevant preclinical models, strongly supporting patient testing.