Department of Endocrinology and Metabolism, National Clinical Research Center for Geriatrics, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, China.
Department of General Surgery and Gastric Cancer Center, Division of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
Hepatology. 2024 Jan 1;79(1):79-95. doi: 10.1097/HEP.0000000000000435. Epub 2023 May 1.
Extrachromosomal circular DNAs (eccDNAs) are prevalent in cancer genomes and emerge as a class of crucial yet less characterized oncogenic drivers. However, the structure, composition, genome-wide frequency, and contribution of eccDNAs in HCC, one of the most fatal and prevalent cancers, remain unexplored. In this study, we provide a comprehensive characterization of eccDNAs in human HCC and demonstrate an oncogenic role of microRNA (miRNA)-17-92-containing eccDNAs in tumor progression.
Using the circle-sequencing method, we identify and characterize more than 230,000 eccDNAs from 4 paired samples of HCC tumor and adjacent nontumor liver tissues. EccDNAs are highly enriched in HCC tumors, preferentially originate from certain chromosomal hotspots, and are correlated with differential gene expression. Particularly, a series of eccDNAs carrying the miRNA-17-92 cluster are validated by outward PCR and Sanger sequencing. Quantitative PCR analyses reveal that miRNA-17-92-containing eccDNAs, along with the expression of their corresponding miRNAs, are elevated in HCC tumors and associated with poor outcomes and the age of HCC patients. More intriguingly, exogenous expression of artificial DNA circles harboring the miR-17-92 cluster, which is synthesized by the ligase-assisted minicircle accumulation method, can significantly accelerate HCC cell proliferation and migration.
These findings delineate the genome-wide eccDNAs profiling of HCC and highlight the functional significance of miRNA-containing eccDNAs in tumorigenesis, providing insight into HCC pathogenesis and cancer therapy, as well as eccDNA and miRNA biology.
外染色体环状 DNA（eccDNA）在癌症基因组中普遍存在，作为一类关键但特征研究较少的致癌驱动因子出现。然而，在 HCC 中，eccDNA 的结构、组成、全基因组频率及其对肿瘤的贡献仍未被探索。本研究全面描绘了 HCC 中的 eccDNA，并证实了 miRNA-17-92 包含的 eccDNA 在肿瘤进展中的致癌作用。
使用 circle-sequencing 方法，我们从 4 对 HCC 肿瘤组织和相邻非肿瘤肝组织样本中鉴定和描绘了超过 230000 个 eccDNA。eccDNA 在 HCC 肿瘤中高度富集，优先来源于特定的染色体热点区域，并与差异基因表达相关。特别地，一系列携带 miRNA-17-92 簇的 eccDNA 通过向外 PCR 和 Sanger 测序得到验证。定量 PCR 分析显示，miRNA-17-92 包含的 eccDNA 及其相应 miRNA 的表达在 HCC 肿瘤中升高，并与不良预后和 HCC 患者的年龄相关。更有趣的是，外源性表达通过连接酶辅助的微小环积累方法合成的含有 miR-17-92 簇的人工 DNA 环可显著加速 HCC 细胞的增殖和迁移。
这些发现描绘了 HCC 的全基因组 eccDNA 图谱，并强调了 miRNA 包含的 eccDNA 在肿瘤发生中的功能意义，为 HCC 的发病机制和癌症治疗以及 eccDNA 和 miRNA 生物学提供了新的见解。
