使用从慢性感染患者获得的肝针活组织检查来绘制组蛋白修

StephenW

J Virol. 2019 Feb 20. pii: JVI.02036-18. doi: 10.1128/JVI.02036-18. [Epub ahead of print]
Mapping the heterogeneity of histone modifications on hepatitis B virus-DNA using liver needle biopsies obtained from chronically infected patients.
Flecken T1,2, Meier MA3, Skewes-Cox P2, Barkan DT2, Heim MH3,4, Wieland SF3, Holdorf MM5.
Author information

1
    Novartis Institutes for Biomedical Research, Infectious Diseases, Emeryville, CA, USA [email protected].
2
    Novartis Institutes for Biomedical Research, CBT Data Sciences, Emeryville, CA, USA.
3
    Department of Biomedicine, University Hospital Basel, University of Basel, Switzerland.
4
    Clinic of Gastroenterology and Hepatology, University Hospital Basel, University of Basel, Switzerland.
5
    Novartis Institutes for Biomedical Research, Infectious Diseases, Emeryville, CA, USA.

Abstract

Covalently closed circular DNA (cccDNA) forms the basis for replication and persistence of hepatitis B virus (HBV) in the chronically infected liver. We have previously shown that viral transcription is subject to regulation by posttranslational modifications (PTMs) of histone proteins bound to cccDNA through analysis of de novo HBV infected cell lines. We now report the successful adaptation of this chromatin immunoprecipitation-sequencing (ChIPseq) approach for analysis of fine-needle patient liver biopsy specimens to investigate the role of histone PTMs in chronically HBV-infected patients. Using 18 specimens from patients in different stages of chronic HBV infection, our work shows that the profile of histone PTMs in chronic infection is more nuanced than previously observed in in vitro models of acute infection. In line with our previous findings, we find that the majority of HBV-derived sequences are associated with the activating histone PTM H3K4me3. However, we show a striking interpatient variability of its deposition in this patient cohort correlated to viral transcription and patient HBV early antigen (HBeAg) status. Unexpectedly, we detect deposition of the classical inhibitory histone PTM H3K9me3 on HBV-DNA in around half of the patient biopsies which could not be linked to reduced levels of viral transcripts. Our results show that current in vitro models are unable to fully recapitulate the complex epigenetic landscape of chronic HBV infection observed in vivo and demonstrate that fine needle liver biopsy specimens can provide sufficient material to further investigate the interaction of viral and host proteins on HBV-DNA.Importance Hepatitis B virus (HBV) is a major global health concern, chronically infecting millions of patients and contributing to a rising burden of liver disease. The viral genome forms the basis for chronic infection and has been shown subject to regulation by epigenetic mechanisms, such as posttranslational modification of histone proteins. Here, we confirm and expand on previous results by adapting a high-resolution technique for analysis of histone modifications to the use with patient-derived fine-needle liver biopsies. Our work highlights that the situation in vivo is more complex than predicted by current in vitro models, for example by suggesting a novel, non-canonical role of the histone modification H3K9me3 in the HBV life cycle. Importantly, enabling the use of fine-needle liver biopsies for such high-resolution analyses may facilitate further research into the epigenetic regulation of the HBV genome.

Copyright © 2019 American Society for Microbiology.

PMID:
    30787147
DOI:
    10.1128/JVI.02036-18

StephenW

J Virol。 2019年2月20日.pii：JVI.02036-18。 doi：10.1128 / JVI.02036-18。 [印刷前的电子版]
使用从慢性感染患者获得的肝针活组织检查来绘制组蛋白修饰对乙型肝炎病毒-DNA的异质性。
Flecken T1,2，Meier MA3，Skewes-Cox P2，Barkan DT2，Heim MH3,4，Wieland SF3，Holdorf MM5。
作者信息

1
    诺华公司生物医学研究所，传染病学院，美国加利福尼亚州埃默里维尔，电子邮件：[email protected]。
2
    诺华公司生物医学研究所，CBT数据科学，美国加利福尼亚州埃默里维尔。
3
    巴塞尔大学医院生物医学系，瑞士巴塞尔大学。
4
    瑞士巴塞尔大学巴塞尔大学医院消化内科和肝脏病学诊所。
五
    诺华公司生物医学研究所，传染病，美国加利福尼亚州埃默里维尔。

抽象

共价闭合环状DNA（cccDNA）形成慢性感染肝脏中乙型肝炎病毒（HBV）复制和持续存在的基础。我们先前已经表明，通过分析新的HBV感染的细胞系，病毒转录受到与cccDNA结合的组蛋白的翻译后修饰（PTM）的调节。我们现在报告成功应用这种染色质免疫沉淀 - 测序（ChIPseq）方法分析细针患者肝活检标本，以研究组蛋白PTM在慢性HBV感染患者中的作用。使用来自慢性HBV感染不同阶段患者的18个样本，我们的工作表明，组蛋白PTM在慢性感染中的分布比先前在急性感染的体外模型中观察到的更细微。与我们先前的发现一致，我们发现大多数HBV衍生的序列与激活组蛋白PTM H3K4me3相关。然而，我们显示其患者队列中的沉积与病毒转录和患者HBV早期抗原（HBeAg）状态相关的惊人的患者间差异。出乎意料的是，我们在约一半的患者活组织检查中检测到经典抑制性组蛋白PTM H3K9me3在HBV-DNA上的沉积，这与病毒转录物水平降低无关。我们的研究结果表明，目前的体外模型无法完全概括体内观察到的慢性HBV感染的复杂表观遗传景观，并证明细针肝活检标本可以提供足够的材料来进一步研究病毒和宿主蛋白在HBV-DNA上的相互作用。重要性乙型肝炎病毒（HBV）是全球主要的健康问题，长期感染数百万患者并导致肝病负担加重。病毒基因组形成慢性感染的基础，并且已显示受到表观遗传机制的调节，例如组蛋白的翻译后修饰。在这里，我们通过采用高分辨率技术分析组蛋白修饰与患者来源的细针肝活组织检查的使用，确认并扩展了之前的结果。我们的工作强调体内情况比当前体外模型预测的更复杂，例如通过提示组蛋白修饰H3K9me3在HBV生命周期中的新的，非规范作用。重要的是，能够使用细针肝活组织检查进行这种高分辨率分析可能有助于进一步研究HBV基因组的表观遗传调控。

版权所有©2019美国微生物学会。

结论：
    30787147
DOI：
    10.1128 / JVI.02036-18