Figure 3 from Selective Depletion of Cancer Cells with Extrachromosomal DNA via Lentiviral Infection

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posted on 2025-08-28, 10:20 authored by Eunhee Yi, Amit D. Gujar, Dacheng Zhao, Kentaro Suina, Xue Jin, Katharina Pardon, Qinghao Yu, Larisa Kagermazova, Emmanuel E. Korsah, Noah A. Dusseau, Jef D. Boeke, Anton G. Henssen, Roel G.W. Verhaak

Alternative ways to deliver transgenes to cells without population shift. A, Larger transgene/plasmid size in lentiviral constructs depletes ecDNA+ cells with the expansion of HSR+ cells. PC3 cells were either untreated or lentivirally transduced with the indicated plasmids for 48 hours and selected with blasticidin for 2 weeks. FISH analysis with the MYC probe was performed to quantify subpopulations (ANOVA, *, P < 0.0001; n = 3). B, Non-lentiviral (PiggyBac) plasmid does not deplete ecDNA+ cells. PC3 cells were either untreated or lentivirally transduced with the Cas9 plasmid (Lenti-Cas9) or transfected with the PiggyBac-Cas9 plasmid for 48 hours and selected with blasticidin for 2 weeks. FISH analysis with the MYC probe was performed to quantify subpopulations (ANOVA, *, P < 0.0001; n = 3).

Funding

Elsa U. Pardee Foundation (EUPF)

National Cancer Institute (NCI)

United States Department of Health and Human Services

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Cancer Research UK (CRUK)

National Institutes of Health (NIH)

Deutsche Krebshilfe (German Cancer Aid)

European Research Council (ERC)

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DOI - Is supplement to Selective Depletion of Cancer Cells with Extrachromosomal DNA via Lentiviral Infection

ARTICLE ABSTRACT

Extrachromosomal DNA (ecDNA), a major focal oncogene amplification mode found across cancer, has recently regained attention as an emerging cancer hallmark, with a pervasive presence across cancers. With technical advancements such as high-coverage sequencing and live-cell genome imaging, we can now investigate the behaviors and functions of ecDNA. However, we still lack an understanding of how to eliminate ecDNA. We observed depletion of cells containing ecDNA during lentiviral but not transposon-based transduction, whereas we sought to investigate the mechanism of ecDNA behavior. This discovery may provide critical information on utilizing a lentiviral system in emerging ecDNA research. Additionally, this observation suggests specific sensitivities for cells with ecDNA. ecDNA is an essential factor in cancer progression. We found that a group of cancer cells with ecDNA is selectively depleted after lentiviral infection. This finding provides promise for ecDNA-specific targeting, suggests the need for caution in using lentivirus, and offers alternative ways to study ecDNA.