Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases

Albeck, 2013, Frequency-modulated pulses of ERK activity transmit quantitative proliferation signals, Mol. Cell, 49, 249, 10.1016/j.molcel.2012.11.002 Aoki, 2013, Stochastic ERK activation induced by noise and cell-to-cell propagation regulates cell density-dependent proliferation, Mol. Cell, 52, 529, 10.1016/j.molcel.2013.09.015 Bak, 1987, Self-organized criticality: an explanation of the 1/f noise, Phys. Rev. Lett., 59, 381, 10.1103/PhysRevLett.59.381 Batchelor, 2011, Stimulus-dependent dynamics of p53 in single cells, Mol. Syst. Biol., 7, 488, 10.1038/msb.2011.20 Batchelor, 2008, Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage, Mol. Cell, 30, 277, 10.1016/j.molcel.2008.03.016 Biggs, 1999, Protein kinase B/Akt-mediated phosphorylation promotes nuclear exclusion of the winged helix transcription factor FKHR1, Proc. Natl. Acad. Sci. USA, 96, 7421, 10.1073/pnas.96.13.7421 Brunet, 1999, Akt promotes cell survival by phosphorylating and inhibiting a Forkhead transcription factor, Cell, 96, 857, 10.1016/S0092-8674(00)80595-4 Brunet, 2002, 14-3-3 transits to the nucleus and participates in dynamic nucleocytoplasmic transport, J. Cell Biol., 156, 817, 10.1083/jcb.200112059 Brunet, 2001, Protein kinase SGK mediates survival signals by phosphorylating the forkhead transcription factor FKHRL1 (FOXO3a), Mol. Cell. Biol., 21, 952, 10.1128/MCB.21.3.952-965.2001 Cai, 2008, Frequency-modulated nuclear localization bursts coordinate gene regulation, Nature, 455, 485, 10.1038/nature07292 Calnan, 2008, The FoxO code, Oncogene, 27, 2276, 10.1038/onc.2008.21 Chen, 2012, A two-dimensional ERK-AKT signaling code for an NGF-triggered cell-fate decision, Mol. Cell, 45, 196, 10.1016/j.molcel.2011.11.023 Cheong, 2011, Information transduction capacity of noisy biochemical signaling networks, Science, 334, 354, 10.1126/science.1204553 Coleman, 1996, An interior trust region approach for nonlinear minimization subject to bounds, SIAM J. Optimization, 6, 418, 10.1137/0806023 De Boor, 2001 Eijkelenboom, 2013, FOXOs: signalling integrators for homeostasis maintenance, Nat. Rev. Mol. Cell Biol., 14, 83, 10.1038/nrm3507 Elowitz, 2000, A synthetic oscillatory network of transcriptional regulators, Nature, 403, 335, 10.1038/35002125 Essers, 2004, FOXO transcription factor activation by oxidative stress mediated by the small GTPase Ral and JNK, EMBO J., 23, 4802, 10.1038/sj.emboj.7600476 Friedman, 2000, Using Bayesian networks to analyze expression data, J. Comput. Biol., 7, 601, 10.1089/106652700750050961 Friedman, 1998, Learning the structure of dynamic probabilistic networks, 139 Geiger, 1994, Learning Gaussian networks, 235 Greer, 2007, The energy sensor AMP-activated protein kinase directly regulates the mammalian FOXO3 transcription factor, J. Biol. Chem., 282, 30107, 10.1074/jbc.M705325200 Gross, 2015, Akt signaling dynamics in individual cells, J. Cell Sci., 128, 2509 Grzegorczyk, 2010, An introduction to Gaussian Bayesian networks, Methods Mol. Biol., 662, 121, 10.1007/978-1-60761-800-3_6 Halford, D., Shoaf, J.H., and Risley, A.S.. (1973). Spectral Density Analysis: Frequency Domain Specification Measurement Signal. Stability. 27th Annual Symposium on Frequency Control, 421–431. Hansen, 2015, Limits on information transduction through amplitude and frequency regulation of transcription factor activity, eLife, 4, 10.7554/eLife.06559 Hansen, 2016, Encoding four gene expression programs in the activation dynamics of a single transcription factor, Curr. Biol., 26, R269, 10.1016/j.cub.2016.02.058 Hao, 2011, Signal-dependent dynamics of transcription factor translocation controls gene expression, Nat. Struct. Mol. Biol., 19, 31, 10.1038/nsmb.2192 Hausdorff, 1996, Multiscaled randomness: a possible source of 1/f noise in biology, Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Top., 54, 2154 Heckerman, 1995, Learning bayesian networks: the combination of knowledge and statistical data, Machine Learn., 20, 197, 10.1007/BF00994016 Hill, 2012, Bayesian inference of signaling network topology in a cancer cell line, Bioinformatics, 28, 2804, 10.1093/bioinformatics/bts514 Hu, 2004, IkappaB kinase promotes tumorigenesis through inhibition of forkhead FOXO3a, Cell, 117, 225, 10.1016/S0092-8674(04)00302-2 Huang, 2006, CDK2-dependent phosphorylation of FOXO1 as an apoptotic response to DNA damage, Science, 314, 294, 10.1126/science.1130512 Jensen, 2011, FoxO3A promotes metabolic adaptation to hypoxia by antagonizing Myc function, EMBO J., 30, 4554, 10.1038/emboj.2011.323 Kamentsky, 2011, Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software, Bioinformatics, 27, 1179, 10.1093/bioinformatics/btr095 Kellogg, 2015, Noise facilitates transcriptional control under dynamic inputs, Cell, 160, 381, 10.1016/j.cell.2015.01.013 Komatsu, 2011, Development of an optimized backbone of FRET biosensors for kinases and GTPases, Mol. Biol. Cell, 22, 4647, 10.1091/mbc.e11-01-0072 Kraskov, 2004, Estimating mutual information, Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 69, 066138, 10.1103/PhysRevE.69.066138 Kreutz, 2007, An error model for protein quantification, Bioinformatics, 23, 2747, 10.1093/bioinformatics/btm397 Lahav, 2004, Dynamics of the p53-Mdm2 feedback loop in individual cells, Nat. Genet., 36, 147, 10.1038/ng1293 Lehtinen, 2006, A conserved MST-FOXO signaling pathway mediates oxidative-stress responses and extends life span, Cell, 125, 987, 10.1016/j.cell.2006.03.046 Lev Bar-Or, 2000, Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study, Proc. Natl. Acad. Sci. USA, 97, 11250, 10.1073/pnas.210171597 Levine, 2013, Functional roles of pulsing in genetic circuits, Science, 342, 1193, 10.1126/science.1239999 Li, 2013, Enantiopure chiral poly(glycerol methacrylate) self-assembled monolayers knock down protein adsorption and cell adhesion, Adv. Healthc. Mater., 2, 1377, 10.1002/adhm.201200402 Lin, 2015, Combinatorial gene regulation by modulation of relative pulse timing, Nature, 527, 54, 10.1038/nature15710 Moelling, 2002, Regulation of Raf-Akt cross-talk, J. Biol. Chem., 277, 31099, 10.1074/jbc.M111974200 Murphy, 2002, 268 Nam, 2009, High levels of Id1 expression define B1 type adult neural stem cells, Cell Stem Cell, 5, 515, 10.1016/j.stem.2009.08.017 Neapolitan, 2004 Nelson, 2004, Oscillations in NF-kappaB signaling control the dynamics of gene expression, Science, 306, 704, 10.1126/science.1099962 Niepel, 2014, Analysis of growth factor signaling in genetically diverse breast cancer lines, BMC Biol., 12, 20, 10.1186/1741-7007-12-20 Novak, 2008, Design principles of biochemical oscillators, Nat. Rev. Mol. Cell Biol., 9, 981, 10.1038/nrm2530 Otsu, 1979, A threshold selection method from gray-level histograms, IEEE Trans. Syst. Man Cybern., 9, 62, 10.1109/TSMC.1979.4310076 Porter, 2016, p53 pulses diversify target gene expression dynamics in an mRNA half-life-dependent manner and delineate Co-regulated target gene subnetworks, Cell Syst., 2, 272, 10.1016/j.cels.2016.03.006 Purvis, 2012, p53 dynamics control cell fate, Science, 336, 1440, 10.1126/science.1218351 Purvis, 2013, Encoding and decoding cellular information through signaling dynamics, Cell, 152, 945, 10.1016/j.cell.2013.02.005 Ramsay, 2009 Ramsay, 2005 Schilling, 2005, Computational processing and error reduction strategies for standardized quantitative data in biological networks, FEBS J., 272, 6400, 10.1111/j.1742-4658.2005.05037.x Senapedis, 2011, Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain, Mol. Biol. Cell, 22, 1791, 10.1091/mbc.e10-10-0854 Sparta, 2015, Receptor level mechanisms are required for epidermal growth factor (EGF)-stimulated extracellular signal-regulated kinase (ERK) activity pulses, J. Biol. Chem., 290, 24784, 10.1074/jbc.M115.662247 Tay, 2010, Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing, Nature, 466, 267, 10.1038/nature09145 Timmer, 2000, Pathological tremors: deterministic chaos or nonlinear stochastic oscillators?, Chaos, 10, 278, 10.1063/1.166494 Tran, 2002, DNA repair pathway stimulated by the forkhead transcription factor FOXO3a through the Gadd45 protein, Science, 296, 530, 10.1126/science.1068712 Traverse, 1994, EGF triggers neuronal differentiation of PC12 cells that overexpress the EGF receptor, Curr. Biol., 4, 694, 10.1016/S0960-9822(00)00154-8 van der Horst, 2007, Stressing the role of FoxO proteins in lifespan and disease, Nat. Rev. Mol. Cell Biol., 8, 440, 10.1038/nrm2190 Yang, 2008, ERK promotes tumorigenesis by inhibiting FOXO3a via MDM2-mediated degradation, Nat. Cell Biol., 10, 138, 10.1038/ncb1676 Yu, 2002, ERK negatively regulates the epidermal growth factor-mediated interaction of Gab1 and the phosphatidylinositol 3-kinase, J. Biol. Chem., 277, 19382, 10.1074/jbc.M200732200