Co-phase separation of KRI1 and NPM1 sustains nucleolar integrity and ribosome biogenesis to fuel liver cancer progression

Liver cancer is the fourth leading cause of global cancer mortality, with hepatocellular carcinoma (HCC) accounting for most primary liver cancers. The nucleolus, as the primary site of ribosome biogenesis, plays a crucial role in HCC development. Here, we report that the nucleolar protein KRR1 interacting protein (KRI1) is aberrantly overexpressed in HCC tissues and interacts with nucleophosmin 1 (NPM1) via phase separation to maintain nucleolar structure and ribosome biogenesis. Downregulation of KRI1 significantly impairs HCC cell proliferation and increases apoptosis, accompanied by disrupted nucleolar structure and ribosome biogenesis. Moreover, we show that KRI1 phase separation is enhanced by the phosphorylation of three serine residues (S94, S95, and S97) in its N-terminal intrinsically disordered region, and pyruvate kinase M2 (PKM2) is identified as the key kinase. PKM2 inhibitor shikonin markedly attenuates KRI1 phase separation and its interaction with NPM1, disrupts nucleolar structure and ribosome biogenesis, thereby inhibiting HCC progression. This study uncovers the crucial role of KRI1 in HCC progression and provides theoretical and experimental evidence for the development of nucleolar protein-targeted therapeutic strategies for HCC treatment.