INSERM U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France.
INSERM U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Strasbourg, France; Université de Strasbourg, Strasbourg, France; Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France.
Gastroenterology. 2019 Jun;156(8):2313-2329.e7. doi: 10.1053/j.gastro.2019.02.038. Epub 2019 Mar 2.
BACKGROUND & AIMS: Chronic hepatitis C virus (HCV) infection is an important risk factor for hepatocellular carcinoma (HCC). Despite effective antiviral therapies, the risk for HCC is decreased but not eliminated after a sustained virologic response (SVR) to direct-acting antiviral (DAA) agents, and the risk is higher in patients with advanced fibrosis. We investigated HCV-induced epigenetic alterations that might affect risk for HCC after DAA treatment in patients and mice with humanized livers.
We performed genome-wide ChIPmentation-based ChIP-Seq and RNA-seq analyses of liver tissues from 6 patients without HCV infection (controls), 18 patients with chronic HCV infection, 8 patients with chronic HCV infection cured by DAA treatment, 13 patients with chronic HCV infection cured by interferon therapy, 4 patients with chronic hepatitis B virus infection, and 7 patients with nonalcoholic steatohepatitis in Europe and Japan. HCV-induced epigenetic modifications were mapped by comparative analyses with modifications associated with other liver disease etiologies. uPA/SCID mice were engrafted with human hepatocytes to create mice with humanized livers and given injections of HCV-infected serum samples from patients; mice were given DAAs to eradicate the virus. Pathways associated with HCC risk were identified by integrative pathway analyses and validated in analyses of paired HCC tissues from 8 patients with an SVR to DAA treatment of HCV infection.
We found chronic HCV infection to induce specific genome-wide changes in H3K27ac, which correlated with changes in expression of mRNAs and proteins. These changes persisted after an SVR to DAAs or interferon-based therapies. Integrative pathway analyses of liver tissues from patients and mice with humanized livers demonstrated that HCV-induced epigenetic alterations were associated with liver cancer risk. Computational analyses associated increased expression of SPHK1 with HCC risk. We validated these findings in an independent cohort of patients with HCV-related cirrhosis (n = 216), a subset of which (n = 21) achieved viral clearance.
In an analysis of liver tissues from patients with and without an SVR to DAA therapy, we identified epigenetic and gene expression alterations associated with risk for HCC. These alterations might be targeted to prevent liver cancer in patients treated for HCV infection.
慢性丙型肝炎病毒（HCV）感染是肝细胞癌（HCC）的一个重要危险因素。尽管有有效的抗病毒治疗，但直接作用抗病毒（DAA）药物治疗后持续病毒学应答（SVR）可降低 HCC 的风险，但在纤维化程度较高的患者中风险仍然较高。我们研究了 DAA 治疗后，在具有人源化肝脏的患者和小鼠中，HCV 引起的表观遗传改变是否会影响 HCC 的风险。
我们对来自欧洲和日本的 6 名无 HCV 感染的患者（对照组）、18 名慢性 HCV 感染患者、8 名慢性 HCV 感染经 DAA 治疗治愈的患者、13 名慢性 HCV 感染经干扰素治疗治愈的患者、4 名慢性乙型肝炎病毒感染患者和 7 名非酒精性脂肪性肝炎患者的肝组织进行了基于全基因组 ChIPmentation 的 ChIP-Seq 和 RNA-seq 分析。通过与其他肝脏疾病病因相关的修饰进行比较分析，绘制 HCV 诱导的表观遗传修饰图谱。我们将 uPA/SCID 小鼠与人肝细胞共移植，创建具有人源化肝脏的小鼠，并给予患者 HCV 感染血清样本注射；给予 DAA 以消灭病毒。通过整合途径分析确定与 HCC 风险相关的途径，并在 8 名 HCV 感染患者对 DAA 治疗获得 SVR 的 HCC 组织的分析中进行验证。
我们发现慢性 HCV 感染可诱导 H3K27ac 的全基因组特异性改变，与 mRNAs 和蛋白质表达的改变相关。这些改变在 DAA 或干扰素为基础的治疗后 SVR 时仍然存在。来自患者和人源化肝脏小鼠的肝组织的整合途径分析表明，HCV 诱导的表观遗传改变与肝癌风险相关。通过计算分析，我们发现 SPHK1 的表达增加与 HCC 风险相关。我们在另一组 HCV 相关肝硬化患者（n=216）中验证了这些发现，其中亚组（n=21）实现了病毒清除。
在对 DAA 治疗后获得 SVR 的患者和未获得 SVR 的患者的肝组织进行分析中，我们确定了与 HCC 风险相关的表观遗传和基因表达改变。这些改变可能成为预防 HCV 感染患者肝癌的靶点。
