HBV整合区的低甲基化通过低通量全基因组亚硫酸氢盐测序帮

StephenW

Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing
Haikun Zhang  1   2 , Peiling Dong  3 , Shicheng Guo  4 , Chengcheng Tao  1 , Wei Chen  1   5 , Wenmin Zhao  3 , Jiakang Wang  6 , Ramsey Cheung  7 , Augusto Villanueva  8 , Jian Fan  1   2 , Huiguo Ding  3 , Steven J Schrodi  9   10 , Dake Zhang  11   12 , Changqing Zeng  13
Affiliations

    PMID: 32741373 DOI: 10.1186/s12916-020-01667-x

Abstract

Background: Circulating cell-free DNA (cfDNA) methylation has been demonstrated to be a promising approach for non-invasive cancer diagnosis. However, the high cost of whole genome bisulfite sequencing (WGBS) hinders the clinical implementation of a methylation-based cfDNA early detection biomarker. We proposed a novel strategy in low-pass WGBS (~ 5 million reads) to detect methylation changes in circulating cell-free DNA (cfDNA) from patients with liver diseases and hepatocellular carcinoma (HCC).

Methods: The effective small sequencing depth were determined by 5 pilot cfDNA samples with relative high-depth WGBS. CfDNA of 51 patients with hepatitis, cirrhosis, and HCC were conducted using low-pass WGBS. The strategy was validated in an independent WGBS cohort of 32 healthy individuals and 26 early-stage HCC patients. Fifteen paired tumor tissue and buffy coat samples were used to characterize the methylation of hepatitis B virus (HBV) integration regions and genome distribution of cfDNA.

Results: A significant enrichment of cfDNA in intergenic and repeat regions, especially in previously reported HBV integration sites were observed, as a feature of cfDNA and the bias of cfDNA release. Methylation profiles nearby HBV integration sites were a better indicator for hypomethylation of tumor genome comparing to Alu and LINE (long interspersed nuclear element) repeats, and were able to facilitate the cfDNA-based HCC prediction. Hypomethylation nearby HBV integration sites (5 kb flanking) was detected in HCC patients, but not in patients with hepatitis and cirrhosis (MethylHBV5k, median:0.61 vs 0.72, P = 0.0003). Methylation levels of integration sites certain candidate regions exhibited an area under the receiver operation curve (AUC) value > 0.85 to discriminate HCC from non-HCC samples. The validation cohort achieved the prediction performance with an AUC of 0.954.

Conclusions: Hypomethylation around viral integration sites aids low-pass cfDNA WGBS to serve as a non-invasive approach for early HCC detection, and inspire future efforts on tumor surveillance for oncovirus with integration activity.

Keywords: Cell-free DNA; DNA methylation; HBV integration; Hepatocellular carcinoma; Low-pass WGBS.

StephenW

HBV整合区的低甲基化通过低通量全基因组亚硫酸氢盐测序帮助无创监测肝细胞癌
张海坤1 2，董炳龄3，郭世成4，陶成城1，陈伟1 5，赵文敏3，王佳康6，张美兰7，奥古斯托维拉纽埃娃8，简繁1 2，丁慧国3，史蒂芬·施罗迪9 10，张大科11 12，曾长青13
隶属关系

    PMID：32741373 DOI：10.1186 / s12916-020-01667-x

抽象

背景：循环无细胞DNA（cfDNA）甲基化已被证明是一种用于非侵入性癌症诊断的有前途的方法。但是，全基因组亚硫酸氢盐测序（WGBS）的高昂成本阻碍了基于甲基化的cfDNA早期检测生物标记物的临床实施。我们提出了一种低通量WGBS（〜500万次读取）的新策略，以检测患有肝病和肝细胞癌（HCC）的患者的循环无细胞DNA（cfDNA）中的甲基化变化。

方法：有效的小测序深度由5个具有相对高深度WGBS的中试cfDNA样品确定。使用低通WGBS对51例肝炎，肝硬化和HCC患者进行CfDNA检测。该策略已在32位健康个体和26位早期HCC患者的独立WGBS队列中得到验证。使用十五对配对的肿瘤组织和血沉棕黄层样本来表征乙型肝炎病毒（HBV）整合区的甲基化和cfDNA的基因组分布。

结果：作为cfDNA的特征和cfDNA释放的偏倚，在基因间和重复区域，特别是在先前报道的HBV整合位点中，cfDNA显着富集。与Alu和LINE（长散布的核元素）重复序列相比，HBV整合位点附近的甲基化图谱是肿瘤基因组低甲基化的更好指标，并且能够促进基于cfDNA的HCC预测。在HCC患者中检测到HBV整合位点附近的甲基化不足（5 kb侧翼），但在肝炎和肝硬化患者中未检测到（甲基HBV5k，中位数：0.61 vs 0.72，P = 0.0003）。某些候选区域的整合位点的甲基化水平在接收器操作曲线（AUC）值> 0.85下显示出面积，以区分HCC与非HCC样品。验证队列以0.954的AUC实现了预测性能。

结论：病毒整合位点周围的甲基化有助于低通cfDNA WGBS用作早期HCC检测的非侵入性方法，并激发了对具有整合活性的癌病毒进行肿瘤监测的未来努力。

关键词：无细胞DNA DNA甲基化； HBV整合；肝细胞癌；低通WGBS。

StephenW

https://bmcmedicine.biomedcentra ... /s12916-020-01667-x