An isogenic cell line panel for sequence-based screening of targeted anticancer drugs

Ashley L Cook; Nicolas Wyhs; Surojit Sur; Blair Ptak; Maria Popoli; Laura Dobbyn; Tasos Papadopoulos; Chetan Bettegowda; Nickolas Papadopoulos; Bert Vogelstein; Shibin Zhou; Kenneth W Kinzler

doi:10.1016/j.isci.2022.104437

An isogenic cell line panel for sequence-based screening of targeted anticancer drugs

iScience. 2022 May 23;25(6):104437. doi: 10.1016/j.isci.2022.104437. eCollection 2022 Jun 17.

Authors

Ashley L Cook^{1

2}, Nicolas Wyhs^{1

3

4}, Surojit Sur^{1

3

4}, Blair Ptak^{3

4}, Maria Popoli¹, Laura Dobbyn³, Tasos Papadopoulos¹, Chetan Bettegowda^{1

3

4

5}, Nickolas Papadopoulos^{1

3

4}, Bert Vogelstein^{1

3

4

6

7}, Shibin Zhou^{1

3

4}, Kenneth W Kinzler^{1

3

4}

Affiliations

¹ Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
² Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
³ Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA.
⁴ Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁵ Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁶ Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
⁷ Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Abstract

We describe the creation of an isogenic cell line panel representing common cancer pathways, with features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cell lines were generated using CRISPR technologies. Surprisingly, most of these lines did not result in complete gene inactivation despite integration of sgRNA at the desired genomic site. A subset of the lines harbored biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterized lines covering 19 frequently lost cancer pathways. 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 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.

Keywords: Biochemical analysis; Biochemistry; Cancer.