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Wittig-Blaich S, Wittig R, Schmidt S, Lyer S, Bewerunge-Hudler M, Gronert-Sum S, Strobel-Freidekind O, Müller C, List M, Jaskot A, Christiansen H, Hafner M, Schadendorf D, Block I, Mollenhauer J. Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma. Oncotarget 2017; 8:23760-23774. [PMID: 28423600 PMCID: PMC5410342 DOI: 10.18632/oncotarget.15863] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/06/2017] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing has dramatically increased genome-wide profiling options and conceptually initiates the possibility for personalized cancer therapy. State-of-the-art sequencing studies yield large candidate gene sets comprising dozens or hundreds of mutated genes. However, few technologies are available for the systematic downstream evaluation of these results to identify novel starting points of future cancer therapies. We improved and extended a site-specific recombination-based system for systematic analysis of the individual functions of a large number of candidate genes. This was facilitated by a novel system for the construction of isogenic constitutive and inducible gain- and loss-of-function cell lines. Additionally, we demonstrate the construction of isogenic cell lines with combinations of the traits for advanced functional in vitro analyses. In a proof-of-concept experiment, a library of 108 isogenic melanoma cell lines was constructed and 8 genes were identified that significantly reduced viability in a discovery screen and in an independent validation screen. Here, we demonstrate the broad applicability of this recombination-based method and we proved its potential to identify new drug targets via the identification of the tumor suppressor DUSP6 as potential synthetic lethal target in melanoma cell lines with BRAF V600E mutations and high DUSP6 expression.
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Affiliation(s)
- Stephanie Wittig-Blaich
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Institute for Comparative Molecular Endocrinology, Ulm University, 89081 Ulm, Germany
| | - Rainer Wittig
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Institute for Laser Technologies in Medicine and Metrology, Ulm University, 89081 Ulm, Germany
| | - Steffen Schmidt
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Stefan Lyer
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Department of Otorhinolaryngology, Section for Experimental Oncology and Nanomedicine (SEON), University Hospital Erlangen, 91054 Erlangen, Germany
| | - Melanie Bewerunge-Hudler
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany.,Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany
| | - Sabine Gronert-Sum
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany
| | - Olga Strobel-Freidekind
- Former Affiliation: Department of Molecular Genome Analysis, German Cancer Research Center (DKFZ), 69118 Heidelberg, Germany
| | - Carolin Müller
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Markus List
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Aleksandra Jaskot
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Helle Christiansen
- Former Affiliation: Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Former Affiliation: Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Mathias Hafner
- Department of Biotechnology, Mannheim University of Applied Sciences, 68163 Mannheim, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Duisburg-Essen, 45147 Essen, Germany and German Cancer Consortium, 69118 Heidelberg, Germany
| | - Ines Block
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark.,Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | - Jan Mollenhauer
- Lundbeckfonden Center of Excellence NanoCAN, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark.,Molecular Oncology, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
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