Targeting cell-state plasticity driven by FOXM1/CEBPB axis disrupts developmental heterogeneity and therapeutic resistance in hepatocellular carcinoma

Abstract

Background & aims: Heterogeneous cellular states traverse the developmental hierarchy induced by phenotypic plasticity and are emerging as key drivers of therapeutic resistance in HCC. However, the factors governing this developmental heterogeneity are not clear, and therapeutic interventions are lacking.

Methods: Autoregulatory network analysis was performed on public datasets of bulk RNA-seq and scRNA-seq data from patients with HCC, as well as on our hepatocyte differentiation model, to identify key transcriptional regulators governing the transition of cellular states during hepatic differentiation. In vitro and in vivo models were used to investigate molecular mechanisms and evaluate therapeutic potential.

Results: We demonstrate dynamic cell-state transitions with chaotic developmental trajectories in the malignant progression of hepatocellular carcinoma. High developmental diversity is closely linked to the activation of drug resistance genes and immune evasion, significantly affecting patient prognosis. We identify that the FOXM1/CEBPB axis at the apex controls developmental heterogeneity dynamics. They form a master decision toggle switch by mutually suppressing each other and competing for control over downstream state-specific networks. Inhibiting FOXM1 restores tumor developmental homogeneity, exposing tumor cells back to immune surveillance. The likely mechanism is the activation of IFN-γ signaling and antigen presentation. A GalNAc-conjugated, chemically modified siRNA lead compound targeting hepatic FOXM1 is designed and shows strong potency and tolerability in therapeutic mouse models.

Conclusion: Tumor cell-state plasticity driven by the FOXM1/CEBPB axis induces developmental heterogeneity and therapeutic resistance in hepatocellular carcinoma. RNAi-based therapies targeting hepatic FOXM1 showed strong potential for further clinical testing.

Impact and implications: Tumor heterogeneity and therapeutic resistance remain major barriers in cancer treatment, largely driven by dynamic transitions across multiple cellular states. This study reveals that the FOXM1/CEBPB axis is a crucial regulator of these hierarchical cellular transitions and plays a key role in sustaining developmental heterogeneity and promoting resistance to therapies. By targeting this axis, we demonstrated the restoration of developmental homogeneity and significant disruption of therapeutic resistance in preclinical models. Furthermore, our findings highlight the strong efficacy of RNAi-based therapeutics directed at hepatic FOXM1, highlighting their promising potential as pioneering small nucleic acid drugs for cancer therapy.

Keywords: Cell–state switch; Drug resistance; RNAi therapy; Tumor heterogeneity; Tumor plasticity.