Integrative 3D genome and epigenomic analysis identifies TP53RK and SYBU as critical regulators of stemness and anti-tumor immunity in HCC.

Three-dimensional (3D) genome organization plays a fundamental role in governing gene regulation and tumor cell properties. However, how higher-order chromatin architecture regulates stemness in hepatocellular carcinoma (HCC) remains unclear. Here, we delineated the 3D chromatin landscapes of well- and poorly differentiated HCC cells and uncovered stemness-associated rewiring of A/B compartmentalization, topologically associating domain (TAD) boundaries, and enhancer-promoter loops. These structural alterations lead to the differential expression of TP53RK and SYBU, which exert opposing effects on HCC stemness and progression. TP53RK promotes tumor stemness by enhancing mitophagy, whereas SYBU suppresses stemness by inhibiting MAPK signaling. Notably, TP53RK expression correlates positively with PD-1, and the combined inhibition of TP53RK and PD-1 markedly enhances anti-tumor immunity. Our findings identify the 3D genome architecture as a key determinant of tumor stemness and highlight TP53RK as a promising therapeutic target in HCC.