Dos Santos Carl Rung, Hansen Lasse Bøllehuus, Rojas-Triana Monica, Johansen Astrid Zedlitz, Perez-Moreno Mirna, Regenberg Birgitte
Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark.
Department of Oncology, Copenhagen University Hospital, Herlev and Gentofte, DK-2730 Herlev, Denmark.
Comput Struct Biotechnol J. 2023 Aug 28;21:4207-4214. doi: 10.1016/j.csbj.2023.08.027. eCollection 2023.
The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the growth of cancer cell lines, questioning the reproducibility of studies utilizing cancer cell line models. Here, we conducted a comprehensive analysis of eccDNA variability in seven cancer cell lines (MCA3D, PDV, HaCa4, CarC, MIA-PaCa-2, AsPC-1, and PC-3). We compared the content of unique eccDNAs between triplicates of each cell line and found that the number of unique eccDNA is specific to each cell line, while the eccDNA sequence content varied greatly among triplicates (∼ 0-1% eccDNA coordinate commonality). In the PC-3 cell line, we found that the large eccDNA (ecDNA) with is present in high-copy number in an NCI cell line isolate but not present in ATCC isolates. Together, these results reveal that the sequence content of eccDNA is highly variable in cancer cell lines. This highlights the importance of testing cancer cell lines before use, and to enrich for subclones in cell lines with the desired eccDNA to get relatively pure population for studying the role of eccDNA in cancer.
携带致癌基因的染色体外环状DNA（eccDNA）的存在与癌症发生及患者不良生存状况密切相关。肿瘤活检组织和癌细胞系常被用作模型来研究eccDNA在癌症中的作用。然而，eccDNA在癌细胞系生长过程中常常丢失，这对利用癌细胞系模型的研究的可重复性提出了质疑。在此，我们对七种癌细胞系（MCA3D、PDV、HaCa4、CarC、MIA-PaCa-2、AsPC-1和PC-3）中的eccDNA变异性进行了全面分析。我们比较了每个细胞系三个重复样本之间独特eccDNA的含量，发现独特eccDNA的数量因细胞系而异，而eccDNA序列含量在三个重复样本之间差异很大（约0-1%的eccDNA坐标一致性）。在PC-3细胞系中，我们发现一种大的eccDNA（ecDNA）在NCI细胞系分离株中以高拷贝数存在，但在ATCC分离株中不存在。总之，这些结果表明eccDNA的序列含量在癌细胞系中高度可变。这突出了在使用前检测癌细胞系的重要性，并在具有所需eccDNA的细胞系中富集亚克隆，以获得相对纯的群体来研究eccDNA在癌症中的作用。
