Single-cell lineage trajectory defines CDK inhibitor-sensitive cells-of-origin in esophageal squamous cell cancer

Understanding the cells of origin is essential for overcoming therapy resistance in esophageal squamous cell carcinoma (ESCC). We utilized machine learning-based single-cell trajectory analysis on 4NQO-induced murine models and genetically engineered organoids to identify multiple distinct cell clusters that serve as cellular origins of ESCC. Gene regulatory network analysis of these populations indicated activation of stem/progenitor cell regulators, including PRRX2 and CEBPβ. Translating these findings, a transcriptome-based drug repurposing screen identified five chemical candidates, four of which are potent Cyclin-Dependent Kinase (CDK) inhibitors, aligning with the frequent loss-of-function mutations in TP53 and CDKN2A observed in ESCC. Notably, CDK inhibitors markedly inhibit ESCC cell proliferation. This research delineates the potential cellular origins of ESCC and their key regulons, thereby pioneering a single-cell-derived therapeutic strategy that exposes vulnerabilities in tumor-initiating cells.