丙型肝炎病毒（HCV）是肝病死亡的主要原因。 HCV 感染如何导致持久的肝损伤并增加癌症风险仍不清楚。在这里，我们将双能肝干细胞确定为丙型肝炎病毒感染的新靶标，并将其错误分化视为肝再生受损和癌症发展的潜在原因。我们展示了由活跃的 HCV 感染个体的肝干细胞产生的 3D 类器官，这些细胞携带复制病毒并在数月内保持低度感染。类器官可以被原发性 HCV 分离株感染。包含病毒的单细胞RNA测序揭示了HCV细胞中的转录重编程支持肝细胞分化、癌症干细胞发育和病毒复制，同时干细胞增殖和干扰素信号传导被破坏。我们的数据在 HCV 感染生物学中添加了一种新的发病机制——肝干细胞感染，这可以解释干细胞状态改变导致的渐进性肝损伤和癌症风险增加。重要性丙型肝炎病毒 (HCV) 会导致肝脏疾病，影响数百万人。 。尽管我们有有效的抗病毒药物可以治愈丙肝病毒，但它们无法阻止晚期肝病。我们使用成体干细胞衍生的肝脏类器官系统来了解丙型肝炎病毒感染如何导致终末期肝病的进展。在这里，我们首次证明丙型肝炎病毒在肝类器官中维持低度感染。肝类器官中的丙型肝炎病毒感染会导致转录重编程，从而导致癌细胞发育和免疫反应改变。我们的研究结果表明，肝类器官中的 HCV 感染如何模仿 HCV 感染和患者的发病机制。这些结果表明，肝类器官中的 HCV 感染会导致肝病进展。

Hepatitis C virus (HCV) is the leading cause of death from liver disease. How HCV infection causes lasting liver damage and increases cancer risk remains unclear. Here, we identify bipotent liver stem cells as novel targets for HCV infection, and their erroneous differentiation as the potential cause of impaired liver regeneration and cancer development. We show 3D organoids generated from liver stem cells from actively HCV-infected individuals carry replicating virus and maintain low-grade infection over months. Organoids can be infected with a primary HCV isolate. Virus-inclusive single-cell RNA sequencing uncovered transcriptional reprogramming in HCV+ cells supporting hepatocytic differentiation, cancer stem cell development, and viral replication while stem cell proliferation and interferon signaling are disrupted. Our data add a new pathogenesis mechanism-infection of liver stem cells-to the biology of HCV infection that may explain progressive liver damage and enhanced cancer risk through an altered stem cell state.ImportanceThe hepatitis C virus (HCV) causes liver disease, affecting millions. Even though we have effective antivirals that cure HCV, they cannot stop terminal liver disease. We used an adult stem cell-derived liver organoid system to understand how HCV infection leads to the progression of terminal liver disease. Here, we show that HCV maintains low-grade infections in liver organoids for the first time. HCV infection in liver organoids leads to transcriptional reprogramming causing cancer cell development and altered immune response. Our finding shows how HCV infection in liver organoids mimics HCV infection and patient pathogenesis. These results reveal that HCV infection in liver organoids contributes to liver disease progression.