Variation of extrachromosomal circular DNA in cancer cell lines
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Variation of extrachromosomal circular DNA in cancer cell lines. / dos Santos, Carl Rung; Hansen, Lasse Bøllehuus; Rojas-Triana, Monica; Johansen, Astrid Zedlitz; Perez-Moreno, Mirna; Regenberg, Birgitte.
In: Computational and Structural Biotechnology Journal, Vol. 21, 2023, p. 4207-4214.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Variation of extrachromosomal circular DNA in cancer cell lines
AU - dos Santos, Carl Rung
AU - Hansen, Lasse Bøllehuus
AU - Rojas-Triana, Monica
AU - Johansen, Astrid Zedlitz
AU - Perez-Moreno, Mirna
AU - Regenberg, Birgitte
N1 - Publisher Copyright: © 2023
PY - 2023
Y1 - 2023
N2 - The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and in vitro cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the in vitro 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 MYC 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.
AB - The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and in vitro cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the in vitro 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 MYC 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.
KW - Cancer cell lines
KW - CNV
KW - Double minute
KW - EccDNA
KW - EcDNA
KW - non-mendelian
KW - Reproducibility
U2 - 10.1016/j.csbj.2023.08.027
DO - 10.1016/j.csbj.2023.08.027
M3 - Journal article
C2 - 37705597
AN - SCOPUS:85169007611
VL - 21
SP - 4207
EP - 4214
JO - Computational and Structural Biotechnology Journal
JF - Computational and Structural Biotechnology Journal
SN - 2001-0370
ER -
ID: 366646134