基于生物信息学的肝癌HBV DNA整合特征研究

doi:10.3877/cma.j.issn.2095-2015.2021.04.003

目的

探讨肝癌HBV DNA整合特征。

方法

结合既往研究中肝癌患者肝癌组织和癌旁组织测序结果，总结其HBV DNA整合位点，通过生物信息学方法分析肝癌组织、癌旁组织中HBV DNA整合位点在染色体水平、重复序列水平、基因水平的分布。利用Bedtools软件计算整合位点与转录活性位点的距离，以探讨整合与转录活性的关系，并比较该特征在肝癌组织、癌旁组织及热点基因组、非热点基因组中的差异。

结果

肝癌组织、癌旁组织中均有HBV DNA整合，其整合位点在染色体水平、重复序列水平和基因水平分布上均存在优势整合。肝癌组织和癌旁组织中分别有8.5%和9.0%的HBV DNA整合位点位于转录活性区域，而随机序列中仅有3.4%。依据泊松分布，在肝癌组织HBV DNA整合基因中鉴定出热点基因。肝癌组织中，热点基因组相较于非热点基因组，更多的HBV DNA整合于高转录活性区域（16.5% vs 3.0%，P<0.001）。

结论

HBV DNA在肝癌组织、癌旁组织中的整合特征不完全相同，但是在肝癌组织、癌旁组织中HBV DNA均倾向于整合至高转录活性区域。

关键词: 肝癌, 乙型肝炎病毒, DNA, 整合

Objective

To investigate the characteristics of hepatitis B virus (HBV) DNA integration in liver cancer.

Methods

Combined with the sequencing results of cancer tissues and adjacent tissues of liver cancer patients in previous studies, the HBV DNA integration sites were summarized, and the distribution of HBV DNA integration sites in liver cancer tissues and adjacent tissues at chromosome level, repetitive sequence level and gene level was analyzed by bioinformatics method. The relationship between integration and transcriptional activity was explored by calculating the distance between integration sites and transcriptional active sites identified by Bedtools software, and the differences of this feature in liver cancer tissues, adjacent tissues, hotspot genome and non-hotspot genome.

Results

HBV DNA integration was found in both liver cancer tissues and adjacent tissues, and the integration sites showed dominant integration at chromosome level, repetitive sequence level, and gene level. In cancer tissues and adjacent tissues, 8.5% and 9.0% of HBV integration sites were located in transcriptional active regions, while only 3.4% of HBV integration sites in random sequences were found. According to Poisson distribution, the hotspot genes were identified in HBV DNA integrated genes in liver cancer tissues. In liver cancer tissues, more HBV DNA was integrated into high transcriptional activity regions in the hotspot genomes than in the non-hotspot genomes (16.5% vs 3.0%, P<0.001).

Conclusion

The integration characteristics of HBV DNA in liver cancer tissues and adjacent tissues are not identical, but in both liver cancer tissues and adjacent tissues, HBV DNA tends to integrate into high transcriptional activity region.

Key words: Liver cancer, Hepatitis B virus, DNA, Integration

图1 HBV DNA在肝癌组织（A）和癌旁组织（B）中的整合情况

图2 HBV DNA在肝癌组织、癌旁组织中的整合模式。图A显示在染色体水平上，肝癌组织（红色）和癌旁组织（绿色）中HBV DNA的整合分布不同；图B显示肝癌组织和癌旁组织在染色体重复序列、基因间、基因内分布不同；图C显示在染色体重复序列子分类中，肝癌组织与癌旁组织不同。SINE为短散在核元件；LINE为长散在核元件；LTR为长末端重复序列；DNA为DNA重复元件；Simple Repeats为简单重复序列；Low Complexity Repeats为低复杂度重复；Satellite Repeats为卫星重复；RNA Repeats为RNA重复序列；Other Repeats为其他；Unknown为未知；图D显示在基因内部，肝癌组织与癌旁组织分布不同

图3 肝癌组织中HBV DNA高频整合的热点基因在全染色体上分布情况及其转录水平。图A显示肝癌组织中HBV DNA整合高频基因在全染色体上的分布。每个柱形表示经log10变换后的整合数量，括号内由左至右依次为基因名、整合数量、整合阳性样本数；图B显示在TCGA库中HBV阳性样本中热点基因在肝癌组织（轨道一：红色）和癌旁组织（轨道一：蓝色）的转录水平

图4 HBV DNA整合位点与转录活性的关系。图A显示不同分组中HBV DNA整合位点与转录活性区域的分布关系，红色表示整合位点落在转录活性区域内，蓝色表示整合位点距离转录活性区域距离1000 bp内，紫色表示整合位点距离转录活性区域1000 bp以外。图B、C显示在距离转录活性位点1000 bp的范围内，在肝癌组织与癌旁组织（B），肝癌组织热点基因与非热点基因区域（C）中，HBV DNA整合位点与转录活性位点的距离分布关系。HCC为肝癌组织组；Paracancer为癌旁组织组；Random为随机序列组；HCC Hotspot为肝癌组织热点基因组，即肝癌组织中HBV DNA高频整合基因组；HCC Dehotspot为肝癌组织非热点基因组，即去除高频整合基因位点后剩余HBV DNA整合基因

1	European Association for the Study of the Liver. EASL Clinical Practice Guidelines: Management of hepatocellular carcinoma [J]. J Hepatol, 2018, 69(1): 182-236.
2	Tu T, Budzinska MA, Vondran FWR, et al. Hepatitis B Virus DNA Integration Occurs Early in the Viral Life Cycle in an In Vitro Infection Model via Sodium Taurocholate Cotransporting Polypeptide-Dependent Uptake of Enveloped Virus Particles [J]. J Virol, 2018, 92(11): e02007-e02017.
3	Chiarle R, Zhang Y, Frock RL, et al. Genome-wide translocation sequencing reveals mechanisms of chromosome breaks and rearrangements in B cells [J]. Cell, 2011, 147(1): 107-119.
4	Gaillard H, Aguilera A. Transcription as a Threat to Genome Integrity [J]. Annu Rev Biochem, 2016, 85: 291-317.
5	Sung WK, Zheng H, Li S, et al. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma [J]. Nat Genet, 2012, 44(7): 765-769.
6	Zhao LH, Liu X, Yan HX, et al. Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma [J]. Nat Commun, 2016, 7: 12992.
7	Furuta M, Tanaka H, Shiraishi Y, et al. Characterization of HBV integration patterns and timing in liver cancer and HBV-infected livers [J]. Oncotarget, 2018, 9(38): 25075-25088.
8	Yang L, Ye S, Zhao X, et al. Molecular Characterization of HBV DNA Integration in Patients with Hepatitis and Hepatocellular Carcinoma [J]. J Cancer, 2018, 9(18): 3225-3235.
9	Weinstein JN, Collisson EA, Mills GB, et al. The Cancer Genome Atlas Pan-Cancer analysis project [J]. Nat Genet, 2013, 45(10): 1113-1120.
10	Xiao R, Chen JY, Liang Z, et al. Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-Based Regulation of Transcription [J]. Cell, 2019, 178(1): 107.e118-121.e118.
11	Yu G, Wang LG, He QY. ChIPseeker: an R/Bioconductor package for ChIP peak annotation，comparison and visualization [J]. Bioinformatics, 2015, 31(14): 2382-2383.
12	Gardini A. Global Run-On Sequencing (GRO-Seq) [J]. Methods Mol Biol, 2017, 1468: 111-120.
13	Tu T, Budzinska MA, Shackel NA, et al. HBV DNA Integration: Molecular Mechanisms and Clinical Implications [J]. Viruses, 2017, 9(4): 75.
14	Lau CC, Sun T, Ching AK, et al. Viral-human chimeric transcript predisposes risk to liver cancer development and progression [J]. Cancer Cell, 2014, 25(3): 335-349.
15	章蔚,严律南.多结节肝细胞癌的研究进展[J].中华肝胆外科杂志, 2016, 22(12): 854-858.
16	何泽宝,陈秋月,朱坚胜,等.慢性乙型肝炎合并肝细胞癌患者乙型肝炎病毒X基因整合对锌指蛋白ZBTB20表达的影响[J].中华传染病杂志, 2019, 37(9): 540-544.
17	Sze KM, Ho DW, Chiu YT, et al. HBV-TERT Promoter Integration Harnesses Host ELF4 Resulting in TERT Gene Transcription in Hepatocellular Carcinoma [J]. Hepatology, 2021, 73(1): 23-40.

[1]	李文琳, 羊玲, 邢凯慧, 陈彩华, 钟丽花, 张娅琴, 张薇. 脐动脉血血气分析联合振幅整合脑电图对新生儿窒息脑损伤的早期诊断价值分析[J]. 中华妇幼临床医学杂志(电子版), 2023, 19(05): 550-558.
[2]	张小曼, 马筱秋, 许正锯, 张纯瑜, 何彩婷. 乙型肝炎病毒逆转录酶区耐药突变对血清乙型肝炎病毒表面抗原水平的影响[J]. 中华实验和临床感染病杂志(电子版), 2023, 17(05): 324-332.
[3]	杨倩, 李翠芳, 张婉秋. 原发性肝癌自发性破裂出血急诊TACE术后的近远期预后及影响因素分析[J]. 中华普外科手术学杂志(电子版), 2024, 18(01): 33-36.
[4]	吴方园, 孙霞, 林昌锋, 张震生. HBV相关肝硬化合并急性上消化道出血的危险因素分析[J]. 中华普外科手术学杂志(电子版), 2024, 18(01): 45-47.
[5]	张文华, 陶焠, 胡添松. 不同部位外生型肝癌临床病理特点及其对术后肝内复发和预后影响[J]. 中华肝脏外科手术学电子杂志, 2023, 12(06): 651-655.
[6]	张海涛, 贾哲, 马超, 张其坤, 武聚山, 郭庆良, 曾道炳, 栗光明, 王孟龙. 手术切除与射频消融治疗血管周围型单发小肝癌临床疗效分析[J]. 中华肝脏外科手术学电子杂志, 2023, 12(05): 523-527.
[7]	李翠平, 陈晓燕, 钱师宇, 林惠珠, 曾彩辉, 阳莉, 卢建溪. 不同抗凝剂保存液对脐血培养的NK细胞增殖及杀伤效应的影响[J]. 中华肝脏外科手术学电子杂志, 2023, 12(05): 572-576.
[8]	韩冰, 顾劲扬. 深度学习神经网络在肝癌诊疗中的研究及应用前景[J]. 中华肝脏外科手术学电子杂志, 2023, 12(05): 480-485.
[9]	葛云鹏, 崔红元, 宋京海. 人工智能在原发性肝癌诊断、治疗及预后中的应用[J]. 中华肝脏外科手术学电子杂志, 2023, 12(04): 367-371.
[10]	赫嵘, 贾哲, 张珂, 李代京, 张萌, 蒋力. 基于PSM分析腹腔镜肝切除联合Hassab术治疗合并门静脉高压症肝癌疗效[J]. 中华肝脏外科手术学电子杂志, 2023, 12(04): 376-383.
[11]	顾睿祈, 方洪生, 蔡国响. 循环肿瘤DNA检测在结直肠癌诊治中的应用与进展[J]. 中华结直肠疾病电子杂志, 2023, 12(06): 453-459.
[12]	丁晨梦, 胡雪慧, 闫沛, 程乔. 髋部骨折术后患者居家康复体验质性研究的Meta整合[J]. 中华老年骨科与康复电子杂志, 2023, 09(06): 365-372.
[13]	杨琬芳, 许晶, 张耀方, 王青, 杨智超, 任方刚, 王宏伟. NK和NKT细胞对急性髓系白血病患者的临床影响[J]. 中华临床医师杂志(电子版), 2023, 17(9): 932-938.
[14]	吴雅琴, 莫伟, 向华, 李琴, 李玉莲, 周碧芳. 肝癌患者介入术后股动脉穿刺处出血的研究进展[J]. 中华介入放射学电子杂志, 2023, 11(04): 352-356.
[15]	于乾雪, 廖学梅, 孙龙龙, 范梦莹, 蒋明超, 孟慧, 李瑞基. 线粒体功能障碍与卵巢早衰的研究进展[J]. 中华诊断学电子杂志, 2023, 11(04): 283-288.

阅读次数

全文

摘要

选择文件类型/文献管理软件名称

选择包含的内容

Characterization of hepatitis B virus DNA integration pattern in liver cancer based on bioinformatics analysis

模态框（Modal）标题

选择文件类型/文献管理软件名称

选择包含的内容

Characterization of hepatitis B virus DNA integration pattern in liver cancer based on bioinformatics analysis