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

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

doi:10.1038/s41598-024-51735-y

Systems BiologyScientific ReportsJan 30, 2024

Peer-reviewed journal article

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

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

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Abstract

Current approaches to define chemical-genetic interactions (CGIs) in human cell lines are resource-intensive. We designed a scalable chemical-genetic screen platform by generating a DNA damage response (DDR)-focused custom sgRNA library. 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 time point interstrand-crosslinking (ICL) repair pathway response to camptothecin-induced DNA damage. Our approach can facilitate screening compounds at scale and produce biologically informative CGI profiles.