Single-Cell Characterization of Terminal States and State-Specific Transcriptional Regulatory Networks in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) exhibits pronounced cellular heterogeneity and dynamic state transitions during tumour progression, yet the emergence of tumour cell states along fate trajectories and their transcriptional regulation remain unclear. Here, we established an integrated framework linking cell fate dynamics with transcriptional regulatory networks using publicly available single-cell RNA sequencing data. Malignant cells were identified by inferred copy number variation, followed by CellRank-based fate inference and SCENIC-based regulatory network reconstruction. We identified three terminal HCC cell states-immune-activated, metabolic, and proliferative hepatocytes-forming a differentiation continuum from stem-like to more mature phenotypes. Each state was governed by a distinct regulatory network with specific core regulators, including IRF3, PPARA, and JUN. Integration with TCGA-LIHC bulk transcriptomic and clinical data revealed that a proliferative state-derived transcriptional signature was associated with poorer overall survival. Together, our study provides a mechanistic framework linking tumour cell fate trajectories, regulatory heterogeneity and clinical outcomes in HCC.