CDK7-targeted therapy effectively disrupts cell cycle progression and oncogenic signaling in head and neck cancer

Head and neck squamous cell carcinoma (HNSCC) remains a prevalent and aggressive malignancy, characterized by a lack of targeted therapies and limited clinical benefits. Here, we conducted an optimized whole-genome CRISPR screen across five HNSCC cell lines aimed at identifying actionable genetic vulnerabilities for rapid preclinical evaluation as novel targeted therapies. Given their critical role in cancer, cyclin-dependent kinases (CDKs) were prioritized for further investigation. Among these, CDK7 was identified as an essential and targetable gene across all five cell lines, prompting its selection for in-depth functional and molecular characterization. Genetic and pharmacological inhibition of CDK7 significantly and consistently reduced tumor cell proliferation due to generalized cell cycle arrest and apoptosis induction. Additionally, CDK7 knockout (KO) and selective inhibitors (YKL-5-124 and samuraciclib) demonstrated potent antitumor activity, effectively suppressing tumor growth in HNSCC patient-derived organoids (PDOs), as well as in both cell line- and patient-derived xenograft (PDX) mouse models with minimal toxicity. Mechanistically, CDK7 inhibition led to a broad downregulation of gene sets related to cell cycle progression and DNA repair, and significantly reduced the transcription of essential genes and untargetable vulnerabilities identified by our CRISPR screen. These findings highlight CDK7 as a promising therapeutic target for HNSCC. Our study provides strong evidence of the robust antitumor activity of CDK7-selective inhibition in disease-relevant preclinical models, strongly supporting its progression to clinical testing. Overall design: Comparative gene expression profiling analysis of RNA-seq data from FaDu cells treated with vehicle, Samuraciclib (250nM) and YKL-5-124 (250nM) for 72h

头颈部鳞状细胞癌（Head and neck squamous cell carcinoma, HNSCC）仍是一种高发且侵袭性极强的恶性肿瘤，当前临床缺乏针对性靶向治疗手段，患者获益有限。本研究针对5株头颈部鳞状细胞癌细胞系开展了优化的全基因组CRISPR筛选，旨在挖掘可用于快速临床前评估的可操作遗传脆弱性，以开发新型靶向疗法。鉴于细胞周期蛋白依赖性激酶（cyclin-dependent kinases, CDKs）在肿瘤发生发展中的核心作用，本研究优先对该类激酶进行后续研究。其中，CDK7被鉴定为在全部5株细胞系中均为必需且可靶向的基因，遂被选中开展深入的功能与分子特征解析。

对CDK7进行遗传干预与药理学抑制，可通过引发广泛的细胞周期阻滞及细胞凋亡，显著且稳定地抑制肿瘤细胞增殖。此外，CDK7基因敲除（knockout, KO）以及选择性抑制剂YKL-5-124与samuraciclib均展现出强效抗肿瘤活性，可有效抑制头颈部鳞状细胞癌患者来源类器官（patient-derived organoids, PDOs）、细胞系来源异种移植模型及患者来源异种移植（patient-derived xenograft, PDX）小鼠模型的肿瘤生长，且毒副作用极低。

机制层面研究显示，CDK7抑制可广泛下调与细胞周期进程及DNA修复相关的基因集，并显著降低本研究CRISPR筛选所鉴定的必需基因与不可靶向脆弱性相关基因的转录水平。上述研究结果表明CDK7是头颈部鳞状细胞癌极具潜力的治疗靶点。本研究为CDK7选择性抑制剂在疾病相关临床前模型中的强效抗肿瘤活性提供了确凿证据，有力支持其推进至临床试验阶段。

总体实验设计：对经溶剂、Samuraciclib（250nM）及YKL-5-124（250nM）处理72小时的FaDu细胞的RNA测序（RNA-seq）数据开展比较基因表达谱分析。