An in vitro CRISPR screen of cell-free DNA identifies apoptosis as the primary mediator of cell-free DNA release

Abtract Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free...

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Published inCommunications biology Vol. 7; no. 1; p. 441
Main Authors Davidson, Brad. A., Miranda, Adam X., Reed, Sarah C., Bergman, Riley E., Kemp, Justin D. J., Reddy, Anvith P., Pantone, Morgan V., Fox, Ethan K., Dorand, R. Dixon, Hurley, Paula J., Croessmann, Sarah, Park, Ben Ho
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 10.04.2024
Nature Publishing Group
Nature Portfolio
Subjects
13
42/35
631/337/4041/3196
631/67/68
631/80/82/23
82
82/1
82/80
96/106
Apoptosis
Biomedical and Life Sciences
Cell lines
CRISPR
Deoxyribonucleic acid
DNA
Genomes
Life Sciences
RNA-binding protein
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Summary:Abtract Clinical circulating cell-free DNA (cfDNA) testing is now routine, however test accuracy remains limited. By understanding the life-cycle of cfDNA, we might identify opportunities to increase test performance. Here, we profile cfDNA release across a 24-cell line panel and utilize a cell-free CRISPR screen (cfCRISPR) to identify mediators of cfDNA release. Our panel outlines two distinct groups of cell lines: one which releases cfDNA fragmented similarly to clinical samples and purported as characteristic of apoptosis, and another which releases larger fragments associated with vesicular or necrotic DNA. Our cfCRISPR screens reveal that genes mediating cfDNA release are primarily involved with apoptosis, but also identify other subsets of genes such as RNA binding proteins as potential regulators of cfDNA release. We observe that both groups of cells lines identified primarily produce cfDNA through apoptosis. These results establish the utility of cfCRISPR, genetically validate apoptosis as a major mediator of DNA release in vitro, and implicate ways to improve cfDNA assays. A novel approach using whole-genome CRISPR-Cas9 screen indicates that apoptosis is the most important mediator of cfDNA release.
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ISSN:2399-3642
2399-3642
DOI:10.1038/s42003-024-06129-1