Systematic decoding of the resistance mechanisms and therapeutic vulnerabilities in TKI-resistant hepatocellular carcinoma

Drug resistance to multiple tyrosine kinase inhibitors (TKIs) is a major issue during clinical management of hepatocellular carcinoma (HCC). Here, through multiplexed in vitro and in vivo CRISPR knockout and base editing screens, we elucidate the resistance mechanisms of HCC to typical TKIs (sorafenib, lenvatinib and regorafenib). Multiple genetic or epigenetic alterations can drive resistance to these TKIs through divergent mechanisms. Among them, a tumor cell-intrinsic (rather than tumor microenvironment-driven) extracellular matrix remodeling mechanism stands out across multiple resistance models and clinical samples. Using druggable gene CRISPR knockout screens, we identify proteasome as a prominent and convergent vulnerability of multiple TKI-resistant HCC cells. We further validate the efficacy of clinically available proteasome inhibitor bortezomib in treating TKI-resistant HCC in multiple preclinical models. Mechanistically, increased p21 expression and dysregulated proteolytic machineries in TKI-resistant tumors account for the pronounced sensitivity to bortezomib. Our work not only delineates a comprehensive landscape of drug resistance mechanisms in TKI-treated HCC, but also suggests actionable therapeutics with immediate clinical potential against these tumors.