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Carazo F, Bértolo C, Castilla C, Cendoya X, Campuzano L, Serrano D, Gimeno M, Planes FJ, Pio R, Montuenga LM, Rubio A. DrugSniper, a Tool to Exploit Loss-Of-Function Screens, Identifies CREBBP as a Predictive Biomarker of VOLASERTIB in Small Cell Lung Carcinoma (SCLC). Cancers (Basel) 2020; 12:E1824. [PMID: 32645997 PMCID: PMC7408696 DOI: 10.3390/cancers12071824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 12/30/2022] Open
Abstract
The development of predictive biomarkers of response to targeted therapies is an unmet clinical need for many antitumoral agents. Recent genome-wide loss-of-function screens, such as RNA interference (RNAi) and CRISPR-Cas9 libraries, are an unprecedented resource to identify novel drug targets, reposition drugs and associate predictive biomarkers in the context of precision oncology. In this work, we have developed and validated a large-scale bioinformatics tool named DrugSniper, which exploits loss-of-function experiments to model the sensitivity of 6237 inhibitors and predict their corresponding biomarkers of sensitivity in 30 tumor types. Applying DrugSniper to small cell lung cancer (SCLC), we identified genes extensively explored in SCLC, such as Aurora kinases or epigenetic agents. Interestingly, the analysis suggested a remarkable vulnerability to polo-like kinase 1 (PLK1) inhibition in CREBBP-mutant SCLC cells. We validated this association in vitro using four mutated and four wild-type SCLC cell lines and two PLK1 inhibitors (Volasertib and BI2536), confirming that the effect of PLK1 inhibitors depended on the mutational status of CREBBP. Besides, DrugSniper was validated in-silico with several known clinically-used treatments, including the sensitivity of Tyrosine Kinase Inhibitors (TKIs) and Vemurafenib to FLT3 and BRAF mutant cells, respectively. These findings show the potential of genome-wide loss-of-function screens to identify new personalized therapeutic hypotheses in SCLC and potentially in other tumors, which is a valuable starting point for further drug development and drug repositioning projects.
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Affiliation(s)
- Fernando Carazo
- Department of Biomedical Engineering and Sciences. School of Engineering, University of Navarra, 20018 San Sebastián, Spain; (F.C.); (C.C.); (X.C.); (M.G.); (F.J.P.)
| | - Cristina Bértolo
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), CIBERONC and Navarra’s Health Research Institute (IDISNA), 31008 Pamplona, Spain; (C.B.); (D.S.); (L.M.M.)
| | - Carlos Castilla
- Department of Biomedical Engineering and Sciences. School of Engineering, University of Navarra, 20018 San Sebastián, Spain; (F.C.); (C.C.); (X.C.); (M.G.); (F.J.P.)
| | - Xabier Cendoya
- Department of Biomedical Engineering and Sciences. School of Engineering, University of Navarra, 20018 San Sebastián, Spain; (F.C.); (C.C.); (X.C.); (M.G.); (F.J.P.)
| | - Lucía Campuzano
- University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg;
| | - Diego Serrano
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), CIBERONC and Navarra’s Health Research Institute (IDISNA), 31008 Pamplona, Spain; (C.B.); (D.S.); (L.M.M.)
- Department of Pathology, Anatomy, and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Marian Gimeno
- Department of Biomedical Engineering and Sciences. School of Engineering, University of Navarra, 20018 San Sebastián, Spain; (F.C.); (C.C.); (X.C.); (M.G.); (F.J.P.)
| | - Francisco J. Planes
- Department of Biomedical Engineering and Sciences. School of Engineering, University of Navarra, 20018 San Sebastián, Spain; (F.C.); (C.C.); (X.C.); (M.G.); (F.J.P.)
| | - Ruben Pio
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), CIBERONC and Navarra’s Health Research Institute (IDISNA), 31008 Pamplona, Spain; (C.B.); (D.S.); (L.M.M.)
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Luis M. Montuenga
- Program in Solid Tumors, Center for Applied Medical Research (CIMA), CIBERONC and Navarra’s Health Research Institute (IDISNA), 31008 Pamplona, Spain; (C.B.); (D.S.); (L.M.M.)
- Department of Pathology, Anatomy, and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Angel Rubio
- Department of Biomedical Engineering and Sciences. School of Engineering, University of Navarra, 20018 San Sebastián, Spain; (F.C.); (C.C.); (X.C.); (M.G.); (F.J.P.)
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