title: A landscape of synthetic viable interactions in cancer.
abstract: Synthetic viability, which is defined as the combination of gene alterations that can rescue the lethal effects of a single gene alteration, may represent a mechanism by which cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in cancer genome to investigate drug resistance are still scarce. Here, we present a computational method to detect synthetic viability-induced drug resistance (SVDR) by integrating the multidimensional data sets, including copy number alteration, whole-exome mutation, expression profile and clinical data. SVDR comprehensively characterized the landscape of SV interactions across 8580 tumors in 32 cancer types by integrating The Cancer Genome Atlas data, small hairpin RNA-based functional experimental data and yeast genetic interaction data. We revealed that the SV interactions are favorable to cells and can predict clinical prognosis for cancer patients, which were robustly observed in an independent data set. By integrating the cancer pharmacogenomics data sets from Cancer Cell Line Encyclopedia (CCLE) and Broad Cancer Therapeutics Response Portal, we have demonstrated that SVDR enables drug resistance prediction and exhibits high reliability between two databases. To our knowledge, SVDR is the first genome-scale data-driven approach for the identification of SV interactions related to drug resistance in cancer cells. This data-driven approach lays the foundation for identifying the genomic markers to predict drug resistance and successfully infers the potential drug combination for anti-cancer therapy.
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yunyan
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Ruiping
authors.initials: R
authors.lastname: Wang
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Han
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Zhangxiang
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Chen
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Fuduan
authors.initials: F
authors.lastname: Peng
authors.affiliation: Department of Pharmacology, Harbin Medical University, Harbin, China.
authors.forename: Haihai
authors.initials: H
authors.lastname: Liang
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Lishuang
authors.initials: L
authors.lastname: Qi
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Zhao
authors.affiliation: Department of Pharmaceutical Sciences and Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA.
authors.forename: Da
authors.initials: D
authors.lastname: Yang
authors.affiliation: Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.|Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
mesh_terms: D019295:Computational Biology / Q000379:methods*; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D020869:Gene Expression Profiling; D005804:Genes, Lethal; D006801:Humans; D009154:Mutation; D009363:Neoplasm Proteins / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism; D010597:Pharmacogenetics
chemical_list: D009363:Neoplasm Proteins