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

iScience (Jun 2022)

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

Affiliations

Ashley L. Cook: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Nicolas Wyhs: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Surojit Sur: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Blair Ptak: Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Maria Popoli: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Laura Dobbyn: Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
Tasos Papadopoulos: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Chetan Bettegowda: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Nickolas Papadopoulos: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Bert Vogelstein: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
Shibin Zhou: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Corresponding author
Kenneth W. Kinzler: Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA; Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Corresponding author

Journal volume & issue: Vol. 25, no. 6
p. 104437

Abstract

Read online

Summary: 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.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

About the journal

Abstract

Keywords