Detection of phenotype-specific therapeutic vulnerabilities in breast cells using a CRISPR loss-of-function screen

The authors would like to thank the laboratory of Dr. Kris C. Wood of the Duke University, which provided resources for the CRISPR knockout screen library, and the University of North Carolina at Chapel Hill where the screen experimental procedures were performed. Further, we thank the RPPA core facility and Dr. Gordon Mills at the MD Anderson Cancer Center (Houston, TX, USA), and the flow cytometry core facility at Oslo University Hospital (Oslo, Norway) for help with the respective analyses. We also want to thank Dr Beata Grallert at the Department of Radiation Biology, Institute for Cancer Research, Oslo University Hospital for sharing STLC and consulting on studies involving cell cycle inhibitors. Finally, we want to gratefully acknowledge Dr Sara Savage at Baylor College of Medicine for her insightful comments and suggestions during the preparation of this manuscript. The work in this manuscript was supported by the following grants: the Norwegian Research Council (Grant #239940) and the Norwegian Cancer Society (Grants #168069, #205222, and #190257), and the National Institutes of Health (R35CA232113, T32CA009156, and F32CA221005). Publisher Copyright: © 2021 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical SocietiesCellular phenotype plasticity between the epithelial and mesenchymal states has been linked to metastasis and heterogeneous responses to cancer therapy, and remains a challenge for the treatment of triple-negative breast cancer (TNBC). Here, we used isogenic human breast epithelial cell lines, D492 and D492M, representing the epithelial and mesenchymal phenotypes, respectively. We employed a CRISPR-Cas9 loss-of-function screen targeting a 2240-gene ‘druggable genome’ to identify phenotype-specific vulnerabilities. Cells with the epithelial phenotype were more vulnerable to the loss of genes related to EGFR-RAS-MAPK signaling, while the mesenchymal-like cells had increased sensitivity to knockout of G2-M cell cycle regulators. Furthermore, we discovered knockouts that sensitize to the mTOR inhibitor everolimus and the chemotherapeutic drug fluorouracil in a phenotype-specific manner. Specifically, loss of EGFR and fatty acid synthase (FASN) increased the effectiveness of the drugs in the epithelial and mesenchymal phenotypes, respectively. These phenotype-associated genetic vulnerabilities were confirmed using targeted inhibitors of EGFR (gefitinib), G2-M transition (STLC), and FASN (Fasnall). In conclusion, a CRISPR-Cas9 loss-of-function screen enables the identification of phenotype-specific genetic vulnerabilities that can pinpoint actionable targets and promising therapeutic combinations.Peer reviewe