An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

Cook, A. L.; Wyhs, N.; Sur, S. B.; Ptak, B.; Popoli, M.; Dobbyn, L.; Papadopoulos, T.; Bettegowda, C.; Papadopoulos, N.; Vogelstein, B.; Zhou, S.; Kinzler, K. W.

doi:10.1101/2021.08.06.455336

bioRxiv · 10.1101/2021.08.06.455336

An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

Cook, A. L.·Wyhs, N.·Sur, S. B.·Ptak, B.·Popoli, M.·Dobbyn, L.·Papadopoulos, T.·Bettegowda, C.·Papadopoulos, N.·Vogelstein, B.·Zhou, S.·Kinzler, K. W.

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Abstract

We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena.

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Cook, A. L., Wyhs, N., Sur, S. B., Ptak, B., Popoli, M., Dobbyn, L., Papadopoulos, T., Bettegowda, C., Papadopoulos, N., Vogelstein, B., Zhou, S., Kinzler, K. W.. 2021-08-08. An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs. https://doi.org/10.1101/2021.08.06.455336

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