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

Lin, K.; Chang, Y.-C.; Billmann, M.; Ward, H. N.; Le, K.; Hassan, A. Z.; Bhojoo, U.; Chan, K.; Costanzo, M.; Moffat, J.; Boone, C.; Bielinsky, A.-K.; Myers, C. L.

doi:10.1101/2023.06.16.545157

bioRxiv · 10.1101/2023.06.16.545157

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

Lin, K.·Chang, Y.-C.·Billmann, M.·Ward, H. N.·Le, K.·Hassan, A. Z.·Bhojoo, U.·Chan, K.·Costanzo, M.·Moffat, J.·Boone, C.·Bielinsky, A.-K.·Myers, C. L.

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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.

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Lin, K., Chang, Y.-C., Billmann, M., Ward, H. N., Le, K., Hassan, A. Z., Bhojoo, U., Chan, K., Costanzo, M., Moffat, J., Boone, C., Bielinsky, A.-K., Myers, C. L.. 2023-06-16. A scalable platform for efficient CRISPR-Cas9 chemical-genetic screens of DNA damage-inducing compounds. https://doi.org/10.1101/2023.06.16.545157

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