Use of a genome-wide haploid genetic screen to identify treatment predicting factors: a proof-of-principle study in pancreatic cancer
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Yuk Ting Ma1,*, Sarah M. Leonard1,*, Naheema Gordon1, Jennifer Anderton1, Claire James1, David Huen2, Ciaran B. Woodman1 and Daniel H. Palmer3
1School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
2Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom
3Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
*These authors have contributed equally to this work
Yuk Ting Ma, email: [email protected]
Keywords: haploid genetic screen, biomarkers, epigenetic therapy, pancreatic cancer
Received: September 27, 2016 Accepted: June 02, 2017 Published: June 29, 2017
The ability to develop a comprehensive panel of treatment predicting factors would significantly improve our ability to stratify patients for cytotoxic or targeted therapies, and prevent patients receiving ineffective treatments. We have investigated if a recently developed genome-wide haploid genetic screen can be used to reveal the critical mediators of response to anticancer therapy. Pancreatic cancer is known to be highly resistant to systemic therapy. Recently epigenetic changes have been shown to be a key determinant in the maintenance of subpopulations of cancer cells with high-level resistance to cytotoxic therapy. We show that in human pancreatic cancer cell lines, treatment with the potent class I histone deacetylase inhibitor, entinostat, synergistically enhances gemcitabine-induced inhibition of cell proliferation and apoptosis. Using a genome-wide haploid genetic screen, we identified deoxycytidine kinase (DCK) as one of the genes with the highest degree of insertional enrichment following treatment with gemcitabine and entinostat; DCK is already known to be the rate-limiting activating enzyme for gemcitabine. Immunoblotting confirmed loss of DCK protein expression in the resistant KBM7 cells. CRISPR/Cas-9 inactivation of DCK in pancreatic cancer cell lines resulted in resistance to gemcitabine alone and in combination with entinostat. We have identified gemcitabine and entinostat as a potential new combination therapy in pancreatic cancer, and in this proof-of-principle study we have demonstrated that a recently developed haploid genetic screen can be used as a novel approach to identify the critical genes that determine treatment response.
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