肿瘤干细胞（CSCs）负责肿瘤的进展和复发。然而，调控肝细胞癌（HCC）干性的机制尚不清楚。应用基因组规模的CRISPR敲除筛选，我们发现H3K4甲基转移酶SETD1A和Trithorax群蛋白的其他成员驱动HCC的肿瘤干性。SETD1A与HCC患者的临床不良结果呈正相关。SETD1A与血清甲胎蛋白的联合使用显著提高了预测HCC复发的准确性。在机械上，SETD1A促进多种修饰组蛋白酶的转录激活，促进H3K4me3和H3K27me3的沉积，活化致癌增强子和超级增强子，从而同时激活致癌基因和失活肿瘤抑制基因在HCC CSCs中。此外，SETD1A与PABPC1相互作用，共同调控致癌基因上的H3K4me3修饰。我们的数据将SETD1A确定为推动HCC干性和进展的关键表观遗传调控因子，突显了SETD1A作为HCC干细胞干预和治疗的候选靶点的潜力。

Cancer stem cells (CSCs) are responsible for tumor progression and recurrence. However, the mechanisms regulating hepatocellular carcinoma (HCC) stemness remain unclear. Applying a genome-scale CRISPR knockout screen, we identify that the H3K4 methyltransferase SETD1A and other members of Trithorax group proteins drive cancer stemness in HCC. SETD1A is positively correlated with poor clinical outcome in HCC patients. Combination of SETD1A and serum AFP significantly improves the accuracy of predicting HCC relapse. Mechanistically, SETD1A mediates transcriptional activation of various histone-modifying enzymes, facilitates deposition of H3K4me3 and H3K27me3 and activates oncogenic enhancers and super-enhancers, leading to activation of oncogenes and inactivation of tumor suppressor genes simultaneously in HCC CSCs. In addition, SETD1A cooperates with PABPC1 to regulate H3K4me3 modification on oncogenes. Our data pinpoint SETD1A as a key epigenetic regulator driving HCC stemness and progression, highlighting the potential of SETD1A as a candidate target for HCC intervention and therapy.