Hepatocellular carcinoma (HCC) develops through multiple mechanisms. While recent studies have shown the presence of extrachromosomal circular DNA (eccDNA) in most cancer types, the eccDNA expression pattern and its association with HCC remain obscure. We aimed to investigate this problem. The genome-wide eccDNA profiles of eight paired HCC and adjacent non-tumor tissue samples were comprehensively elucidated based on Circle-seq, and they were further cross-analyzed with the RNA sequencing data to determine the association between eccDNA expression and transcriptome dysregulation. A total of 60,423 unique eccDNA types were identified. Most of the detected eccDNAs were smaller than 1 kb, with a length up to 182,363 bp and a mean sizes of 674 bp (non-tumor) and 813 bp (tumor), showing a greater association with gene-rich rather than with gene-poor regions. Although there was no statistical difference in length and chromosome distribution, the eccDNA patterns between HCC and adjacent non-tumor tissues showed significant differences at both the chromosomal and single gene levels. Five of the eight HCC tissues showed significantly higher amounts of chromosome 22-derived eccDNA expression compared to the non-tumor tissue. Furthermore, two genes, SLC16A3 and BAIAP2L2, with a higher transcription level in tumor tissues, were related to eccDNAs exclusively detected in three HCC samples and were negatively associated with survival rates in HCC cohorts from public databases. These results indicate the existence and massive heterogeneity of eccDNAs in HCC and adjacent liver tissues, and suggest their potential association with dysregulated gene expression.
肝细胞癌（HCC）的发生涉及多种机制。尽管近期研究显示大多数癌症类型中存在染色体外环状DNA（eccDNA），但eccDNA的表达模式及其与HCC的关联尚不明确。本研究旨在探讨这一问题。基于Circle-seq技术，我们全面解析了八对HCC组织及癌旁非肿瘤组织的全基因组eccDNA谱，并进一步结合RNA测序数据进行交叉分析，以探究eccDNA表达与转录组失调之间的关联。共鉴定出60,423种独特的eccDNA类型。检测到的大多数eccDNA长度小于1kb，最大可达182,363bp，平均长度分别为674bp（非肿瘤组织）和813bp（肿瘤组织），且更倾向于富集于基因密集区域而非基因稀疏区域。尽管在长度和染色体分布上无统计学差异，但HCC组织与癌旁非肿瘤组织间的eccDNA模式在染色体和单基因水平均呈现显著差异。八例HCC组织中有五例显示出显著高于非肿瘤组织的22号染色体来源eccDNA表达。此外，在肿瘤组织中转录水平更高的SLC16A3和BAIAP2L2两个基因，与仅在三个HCC样本中检测到的eccDNA相关，且这两个基因在公共数据库的HCC队列中与患者生存率呈负相关。这些结果表明HCC及癌旁肝组织中存在eccDNA且具有高度异质性，提示其可能与基因表达失调存在潜在关联。
肿瘤(癌症)患者之家