Novartis Institutes for Biomedical Research, Infectious Diseases, Emeryville, California, USA
Novartis Institutes for Biomedical Research, CBT Data Sciences, Emeryville, California, USA.
J Virol. 2019 Apr 17;93(9). doi: 10.1128/JVI.02036-18. Print 2019 May 1.
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 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 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 with viral transcription and patient HBV early antigen (HBeAg) status. Unexpectedly, we detected deposition of the classical inhibitory histone PTM H3K9me3 on HBV-DNA in around half of the patient biopsy specimens, which could not be linked to reduced levels of viral transcripts. Our results show that current models are unable to fully recapitulate the complex epigenetic landscape of chronic HBV infection observed 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. 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 to be 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 for use with patient-derived fine-needle liver biopsy specimens. Our work highlights that the situation is more complex than predicted by current models, for example, by suggesting a novel, noncanonical role of the histone modification H3K9me3 in the HBV life cycle. Importantly, enabling the use of fine-needle liver biopsy specimens for such high-resolution analyses may facilitate further research into the epigenetic regulation of the HBV genome.
共价闭合环状 DNA (cccDNA) 是乙型肝炎病毒 (HBV) 在慢性感染肝脏中复制和持续存在的基础。我们之前通过分析 HBV 感染的细胞系表明，病毒转录受结合到 cccDNA 的组蛋白蛋白的翻译后修饰 (PTM) 调节。我们现在报告说，我们已经成功地将这种染色质免疫沉淀测序 (ChIPseq) 方法适应于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 感染不同阶段的 18 个患者标本，我们的工作表明，与我们之前在急性感染模型中观察到的情况相比，慢性感染中的组蛋白 PTM 谱更为复杂。与我们之前的发现一致，我们发现大多数 HBV 衍生序列与激活组蛋白 PTM H3K4me3 相关。然而，我们在该患者队列中发现其沉积的惊人的个体间变异性与病毒转录和患者 HBV 早期抗原 (HBeAg) 状态相关。出乎意料的是，我们在大约一半的患者活检标本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。我们的结果表明，目前的模型无法完全再现慢性 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。乙型肝炎病毒 (HBV) 是一个全球性的健康问题，它慢性感染着数百万患者，并导致肝病负担不断增加。病毒基因组是慢性感染的基础，并且已经被证明受到表观遗传机制的调节，例如组蛋白蛋白的翻译后修饰。在这里，我们通过适应用于分析组蛋白修饰的高分辨率技术来确认和扩展以前的结果，该技术用于使用源自患者的细针肝活检标本。我们的工作强调了这种情况比当前的模型预测的更为复杂，例如，建议组蛋白修饰 H3K9me3 在 HBV 生命周期中具有新的、非典型的作用。重要的是，能够使用细针肝活检标本进行这种高分辨率分析可能会促进对 HBV 基因组的表观遗传调控的进一步研究。
