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

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

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