Network Analysis Reveals A Signaling Regulatory Loop in the PIK3CA-mutated Breast Cancer Predicting Survival Outcome

Carter, 2009, Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations, Cancer Res, 69, 6660, 10.1158/0008-5472.CAN-09-1133 Kandoth, 2013, Mutational landscape and significance across 12 major cancer types, Nature, 502, 333, 10.1038/nature12634 Komen SG. Molecular subtypes of breast cancer. [Internet] 2014 [cited 2015 Oct 13]. Available from: http://ww5.komen.org/BreastCancer/SubtypesofBreastCancer.html. Hanahan, 2000, The hallmarks of cancer, Cell, 100, 57, 10.1016/S0092-8674(00)81683-9 Wang, 2015, Predictive genomics: a cancer hallmark network framework for predicting tumor clinical phenotypes using genome sequencing data, Semin Cancer Biol, 30, 4, 10.1016/j.semcancer.2014.04.002 Cui, 2007, A map of human cancer signaling, Mol Syst Biol, 3, 152, 10.1038/msb4100200 Samuels, 2010, Oncogenic mutations of PIK3CA in human cancers, Curr Top Microbiol Immunol, 347, 21 Barabási, 2004, Network biology: understanding the cell’s functional organization, Nat Rev Genet, 5, 101, 10.1038/nrg1272 Li, 2012, The human phosphotyrosine signaling network: evolution and hotspots of hijacking in cancer, Genome Res, 22, 1222, 10.1101/gr.128819.111 Babu, 2004, Structure and evolution of transcriptional regulatory networks, Curr Opin Struct Biol, 14, 283, 10.1016/j.sbi.2004.05.004 Wang, 2005, Network motifs are enriched with transcription factors whose transcripts have short half-lives, Trends Genet, 21, 492, 10.1016/j.tig.2005.06.013 Cloutier, 2011, Dynamic modeling and analysis of cancer cellular network motifs, Integr Biol (Camb), 3, 724, 10.1039/c0ib00145g Cui, 2006, Principles of microRNA regulation of a human cellular signaling network, Mol Syst Biol, 2, 46, 10.1038/msb4100089 Fu, 2009, Signaling network analysis of ubiquitin-mediated proteins suggests correlations between the 26S proteasome and tumor progression, Mol Biosyst, 5, 1809, 10.1039/b905382d Paliouras, 2011, Dynamic rewiring of the androgen receptor protein interaction network correlates with prostate cancer clinical outcomes, Integr Biol (Camb), 3, 1020, 10.1039/c1ib00038a Zaman, 2015, Signaling network assessment of mutations and copy number variations predict breast cancer subtype-specific drug targets, Cell Rep, 5, 216, 10.1016/j.celrep.2013.08.028 Gao, 2016, Identification and construction of combinatory cancer hallmark-based gene signature sets to predict recurrence and chemotherapy benefit in stage II colorectal cancer, JAMA Oncol, 2, 37, 10.1001/jamaoncol.2015.3413 Milo, 2002, Network motifs: simple building blocks of complex networks, Science, 298, 824, 10.1126/science.298.5594.824 Awan, 2007, Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network, IET Syst Biol, 1, 292, 10.1049/iet-syb:20060068 Heldin, 2013, Targeting the PDGF signaling pathway in tumor treatment, Cell Commun Signal, 11, 97, 10.1186/1478-811X-11-97 Waltenberger, 1994, Different signal transduction properties of KDR and Flt1, two receptors for vascular endothelial growth factor, J Biol Chem, 269, 26988, 10.1016/S0021-9258(18)47116-5 Zheng, 2013, Temporal regulation of EGF signalling networks by the scaffold protein Shc1, Nature, 499, 166, 10.1038/nature12308 Neumann-Haefelin, 2008, SHC-1/p52Shc targets the insulin/IGF-1 and JNK signaling pathways to modulate life span and stress response in C. elegans, Genes Dev, 22, 2721, 10.1101/gad.478408 Martín, 2013, PAM50 proliferation score as a predictor of weekly paclitaxel benefit in breast cancer, Breast Cancer Res Treat, 138, 457, 10.1007/s10549-013-2416-2 Nielsen, 2010, A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer, Clin Cancer Res, 16, 5222, 10.1158/1078-0432.CCR-10-1282 Galimov, 2010, The role of p66shc in oxidative stress and apoptosis, Acta Naturae, 2, 44, 10.32607/20758251-2010-2-4-44-51 Hudson, 2014, P66ShcA promotes breast cancer plasticity by inducing an epithelial-to-mesenchymal transition, Mol Cell Biol, 34, 3689, 10.1128/MCB.00341-14 Wu, 2015, FDA-approved small-molecule kinase inhibitors, Trends Pharmacol Sci, 36, 422, 10.1016/j.tips.2015.04.005 Fischer, 2008, FLT1 and its ligands VEGFB and PlGF: drug targets for anti-angiogenic therapy?, Nat Rev Cancer, 8, 942, 10.1038/nrc2524 Day, 2013, PIK3CA and PTEN gene and exon mutation-specific clinicopathologic and molecular associations in colorectal cancer, Clin Cancer Res, 19, 3285, 10.1158/1078-0432.CCR-12-3614 Di Nicolantonio, 2010, Deregulation of the PI3K and KRAS signaling pathways in human cancer cells determines their response to everolimus, J Clin Invest, 120, 2858, 10.1172/JCI37539 Koh, 2012, COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines, Nucleic Acids Res, 40, D957, 10.1093/nar/gkr959 Marcotte, 2012, Essential gene profiles in breast, pancreatic, and ovarian cancer cells, Cancer Discov, 2, 172, 10.1158/2159-8290.CD-11-0224 Forbes, 2011, COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer, Nucleic Acids Res, 39, D945, 10.1093/nar/gkq929 Mermel, 2011, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biol, 12, R41, 10.1186/gb-2011-12-4-r41 Barretina, 2012, The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity, Nature, 483, 603, 10.1038/nature11003 Li, 2010, Identification of high-quality cancer prognostic markers and metastasis network modules, Nat Commun, 1, 34, 10.1038/ncomms1033