Changes in gene expression variability reveal a stable synthetic lethal interaction network in BRCA2−ovarian cancers

Chan, 2011, Harnessing synthetic lethal interactions in anticancer drug discovery, Nat. Rev. Drug Discov., 10, 351, 10.1038/nrd3374 Nijman, 2011, Synthetic lethality: general principles, utility and detection using genetic screens in human cells, FEBS Lett., 585, 1, 10.1016/j.febslet.2010.11.024 Reinhardt, 2009, Exploiting synthetic lethal interactions for targeted cancer therapy, Cell Cycle, 8, 3112, 10.4161/cc.8.19.9626 Dobzhansky, 1946, Genetics of natural populations. Xiii. Recombination and variability in populations of Drosophila Pseudoobscura, Genetics, 31, 269, 10.1093/genetics/31.3.269 Lucchesi, 1968, Synthetic lethality and semi-lethality among functionally related mutants of Drosophila melanogaster, Genetics, 59, 37, 10.1093/genetics/59.1.37 Kaelin, 2005, The concept of synthetic lethality in the context of anticancer therapy, Nat. Rev. Cancer, 5, 689, 10.1038/nrc1691 Hartman, 2001, Principles for the buffering of genetic variation, Science, 291, 1001, 10.1126/science.291.5506.1001 Friend, 1998, Emerging uses for genomic information in drug discovery, N. Engl. J. Med., 338, 125, 10.1056/NEJM199801083380211 Hartwell, 1997, Integrating genetic approaches into the discovery of anticancer drugs, Science, 278, 1064, 10.1126/science.278.5340.1064 Blomen, 2015, Gene essentiality and synthetic lethality in haploid human cells, Science, 350, 1092, 10.1126/science.aac7557 Gudmundsdottir, 2006, The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability, Oncogene, 25, 5864, 10.1038/sj.onc.1209874 Roy, 2011, BRCA1 and BRCA2: different roles in a common pathway of genome protection, Nat. Rev. Cancer, 12, 68, 10.1038/nrc3181 Turner, 2007, BRCA1 dysfunction in sporadic basal-like breast cancer, Oncogene, 26, 2126, 10.1038/sj.onc.1210014 Tutt, 2002, The relationship between the roles of BRCA genes in DNA repair and cancer predisposition, Trends Mol. Med., 8, 571, 10.1016/S1471-4914(02)02434-6 Farmer, 2005, Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy, Nature, 434, 917, 10.1038/nature03445 Fong, 2009, Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers, N. Engl. J. Med., 361, 123, 10.1056/NEJMoa0900212 Gibson, 2012, New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs, Nat. Rev. Mol. Cell Biol., 13, 411, 10.1038/nrm3376 Shaheen, 2011, Synthetic lethality: exploiting the addiction of cancer to DNA repair, Blood, 117, 6074, 10.1182/blood-2011-01-313734 Turner, 2005, Targeting the DNA repair defect of BRCA tumours, Curr. Opin. Pharmacol., 5, 388, 10.1016/j.coph.2005.03.006 Roy, 2012, BRCA1 and BRCA2: different roles in a common pathway of genome protection, Nat. Rev. Cancer, 12, 68, 10.1038/nrc3181 Ashworth, 2008, A synthetic lethal therapeutic approach: poly(ADP) ribose polymerase inhibitors for the treatment of cancers deficient in DNA double-strand break repair, J. Clin. Oncol., 26, 3785, 10.1200/JCO.2008.16.0812 Edwards, 2008, Resistance to therapy caused by intragenic deletion in BRCA2, Nature, 451, 1111, 10.1038/nature06548 Sakai, 2008, Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers, Nature, 451, 1116, 10.1038/nature06633 Ryan, 2014, DAISY: picking synthetic lethals from cancer genomes, Cancer Cell, 26, 306, 10.1016/j.ccr.2014.08.008 Wang, 2013, Identification of potential synthetic lethal genes to p53 using a computational biology approach, BMC Med. Genomics, 6, 30, 10.1186/1755-8794-6-30 Aly, 2011, BRCA1, PARP, and 53BP1: conditional synthetic lethality and synthetic viability, J. Mol. Cell Biol., 3, 66, 10.1093/jmcb/mjq055 Luo, 2009, A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene, Cell, 137, 835, 10.1016/j.cell.2009.05.006 Srihari, 2015, Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer, Biol. Direct, 10, 57, 10.1186/s13062-015-0086-1 Wappett, 2016, Multi-omic measurement of mutually exclusive loss-of-function enriches for candidate synthetic lethal gene pairs, BMC Genomics, 17, 65, 10.1186/s12864-016-2375-1 Burga, 2011, Predicting mutation outcome from early stochastic variation in genetic interaction partners, Nature, 480, 250, 10.1038/nature10665 de Torrente, 2017, pathVar: a new method for pathway-based interpretation of gene expression variability, Peer J., 5, e3334, 10.7717/peerj.3334 Trapnell, 2010, Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation, Nat. Biotechnol., 28, 511, 10.1038/nbt.1621 Durinck, 2005, BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis, Bioinformatics, 21, 3439, 10.1093/bioinformatics/bti525 Gao, 2013, Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal, Sci. Signal., 6, l1, 10.1126/scisignal.2004088 Cerami, 2012 Network TCGAR, 2011, Integrated genomic analyses of ovarian carcinoma, Nature, 474, 609, 10.1038/nature10166 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. Royal Statis. Soc. Series B (Methodological), 57, 289, 10.1111/j.2517-6161.1995.tb02031.x Guo, 2016, SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets, Nucl. Acids Res., 44, D1011, 10.1093/nar/gkv1108 Prasad, 2009, Human protein reference database—2009 update, Nucl. Acids Res., 37, D767, 10.1093/nar/gkn892 Csardi, 2006, The igraph software package for complex network research, Inter J. Complex Syst., 1695, 1 Team RC: R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2015, URL http. www R-project org, 2016. Team RC: R: A language and environment for statistical computing. R. Foundation for Statistical Computing, in: Vienna, Austria, 2016. Hasegawa, 2015, Variability of gene expression identifies transcriptional regulators of early human embryonic development, PLoS Genet., 11, e1005428, 10.1371/journal.pgen.1005428 Yu, 2008, A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers, PLoS Genet., 4, e1000129, 10.1371/journal.pgen.1000129 Dai, 2010, New insights into checkpoint kinase 1 in the DNA damage response signaling network, Clin. Cancer Res., 16, 376, 10.1158/1078-0432.CCR-09-1029 Helleday, 2008, DNA repair pathways as targets for cancer therapy, Nat. Rev. Cancer, 8, 193, 10.1038/nrc2342 Avantaggiati, 1997, Recruitment of p300/CBP in p53-dependent signal pathways, Cell, 89, 1175, 10.1016/S0092-8674(00)80304-9 Hanahan, 2011, Hallmarks of cancer: the next generation, Cell, 144, 646, 10.1016/j.cell.2011.02.013 Park, 2015, Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types, Mol. Syst. Biol., 11, 824, 10.15252/msb.20156102 Lin, 1998, The evolutionarily conserved zinc finger motif in the largest subunit of human replication protein A is required for DNA replication and mismatch repair but not for nucleotide excision repair, J. Biol. Chem., 273, 1453, 10.1074/jbc.273.3.1453 Bochkareva, 2002, Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA, EMBO J., 21, 1855, 10.1093/emboj/21.7.1855 Kitano, 2003, Cancer robustness: tumour tactics, Nature, 426, 125, 10.1038/426125a Kitano, 2004, Cancer as a robust system: implications for anticancer therapy, Nat. Rev. Cancer, 4, 227, 10.1038/nrc1300