A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds

Kevin Lin, Ya Chu Chang, Maximilian Billmann, Henry N. Ward, Khoi Le, Arshia Z. Hassan, Urvi Bhojoo, Katherine Chan, Michael Costanzo, Jason Moffat, Charles Boone, Anja Katrin Bielinsky, Chad L. Myers

Research output: Contribution to journalArticlepeer-review

Abstract

Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screening platform by generating a DNA damage response (DDR)-focused custom sgRNA library targeting 1011 genes with 3033 sgRNAs. We performed five proof-of-principle compound screens and found that the compounds’ known modes-of-action (MoA) were enriched among the compounds’ CGIs. These scalable screens recapitulated expected CGIs at a comparable signal-to-noise ratio (SNR) relative to genome-wide screens. Furthermore, time-resolved CGIs, captured by sequencing screens at various time points, suggested an unexpected, late interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale with 20-fold fewer resources than commonly used genome-wide libraries and produce biologically informative CGI profiles.

Original languageEnglish (US)
Article number2508
JournalScientific reports
Volume14
Issue number1
DOIs
StatePublished - Dec 2024

Bibliographical note

Publisher Copyright:
© 2024, The Author(s).

PubMed: MeSH publication types

  • Journal Article

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