Computational Analyses of Synergism in Small Molecular Network Motifs

PLoS Computational Biology

Volumn 10, Issue 3, 2014, Pages

  Zhang, Yili ^a   Smolen, Paul ^a   Baxter, Douglas A ^a   Byrne, John H ^a  

^a UNIVERSITY OF TEXAS MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX NETWORKS; NETWORK ARCHITECTURE;

CELLULAR FUNCTION; CELLULAR RESPONSE; COMPLEX REGULATORY NETWORK; COMPUTATIONAL ANALYSIS; DYNAMICAL PROPERTIES; DYNAMICAL RESPONSE; INTUITIVE UNDERSTANDING; MOLECULAR COMPONENTS; MOLECULAR NETWORKS; NETWORK MOTIF;

BLENDING;

ACTIVATING TRANSCRIPTION FACTOR 4; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN;

ANALYTICAL PARAMETERS; ARTICLE; BIOLOGICAL MODEL; CONTROLLED STUDY; DRUG ANTAGONISM; DRUG POTENTIATION; MATHEMATICAL COMPUTING; MOLECULAR DYNAMICS; MOLECULAR LIBRARY; MOLECULAR MECHANICS; NEGATIVE FEEDBACK; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN SYNTHESIS; PROTEIN SYNTHESIS REGULATION; PROTEIN TARGETING; QUANTITATIVE ANALYSIS; STIMULUS RESPONSE;

AMINO ACID MOTIFS; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CREB-BINDING PROTEIN; CYCLIC AMP RESPONSE ELEMENT-BINDING PROTEIN; DRUG THERAPY, COMBINATION; FEEDBACK, PHYSIOLOGICAL; GENE REGULATORY NETWORKS; GENES, BACTERIAL; HUMANS; SOFTWARE; SYSTEMS BIOLOGY; TRANSCRIPTION, GENETIC;

EID: 84897371312     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003524     Document Type: Article

References (58)

1. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chkiovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824-827.
2. Goemann B, Wingender E, Potapov AP, (2009) An approach to evaluate the topological significance of motifs and other patterns in regulatory networks. BMC Syst Biol 3: 53 doi:10.1186/1752-0509-3-53.
3. Kaizu K, Ghosh S, Matsuoka Y, Moriya H, Shimizu-Yoshida Y, et al. (2010) A comprehensive molecular interaction map of the yeast cell cycle. Mol Syst Biol 6: 415 doi:10.1038/msb.2010.73.
4. Cui Q, Ma Y, Jaramillo M, Bari H, Awan A, et al. (2007) A map of human cancer signaling. Mol Syst Biol 3: 152 doi:10.103/msb4100200.
5. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489: 91-100.
6. Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al. (2005) Core transcription regulatory circuitry in human embryonic stem cells. Cell 122: 947-956.
7. Cloutier M, Wang E, (2011) Dynamic modeling and analysis of cancer cellular network motifs. Integr Biolo (Camb) 3: 724-732.
8. Lim WA, Lee CM, Tang C, (2013) Design principles of regulatory networks: searching for the molecular algorithms of the cell. Cell 49: 202-212.
9. Odom DT, Zizlsperger N, Gordon DB, Bell GW, Rinaldi NJ, et al. (2004) Control of pancreas and liver gene expression by HNF transcription factors. Science 303: 1378-1381.
10. Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD, (2012) Asymmetric positive feedback loops reliably control biological responses. Mol Syst Biol 8: 577.
11. Shellman ER, Burant CF, Schnell S, (2013) Network motifs provide signatures that characterize metabolism. Mol Biosyst 9: 352-360.
12. Wu SF, Qian WY, Zhang JW, Yang YB, Liu Y, et al. (2013) Network motifs in the transcriptional regulation network of cervical carcinoma cells respond to EGF. Arch Gynecol Obstet 287: 771-777.
13. Alon U, (2007) Networks motifs: theory and experimental approaches. Nat Rev Genet 8: 450-461.
14. Fioravanti F, Helmer-Citterich M, Nardelli E, (2012) Modeling gene regulatory network motifs using Statecharts. BMC Bioinformatic 13 (Suppl 4) (): S20 doi:10.1186/1471-2105-13-S4-S20.
15. Han Z, Voldriska TM, Yang L, MacLellan WR, Weiss JN, Qu Z, (2007) Signal transduction network motifs and biological memory. J Theor Biol 246: 755-761.
16. Mangan S, Itzkovitz S, Zaslaver A, Alon U, (2005) The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli. J Mol Biol 356: 1073-1081.
17. Smolen P, Baxter DA, Byrne JH, (2000) Mathematical modeling of gene networks. Neuron 26: 567-580.
18. Kaplan S, Bren A, Dekel E, Alon U, (2008) The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol 4: 203-210.
19. Madar D, Dekel E, Bren A, Alon U, (2011) Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli. BMC Syst Biol 5: 111.
20. Tian XJ, Zhang XP, Liu F, Wang W, (2009) Interlinking positive and negative feedback loops create a tunable motif in gene regulatory networks. Phys Rev E Stat Nonlin Soft Matter Phys 80: 011926.
21. Zhang S, Jin G, Zhang XS, Chen L, (2007) Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics 7: 2856-2869.
22. Awan A, Bari H, Yan F, Moksong S, Yang S, et al. (2007) Regulatory network motifs and hotspots of cancer genes in mammalian cellular signaling network. IET Syst Biol 1: 292-297.
23. Liu ZP, Wang Y, Zhang XS, Chen L, (2012) Network-based analysis of complex diseases. IET Syst Biol 6: 22-33.
24. Liu R-Y, Zhang Y, Baxter DA, Smolen P, Cleary LJ, et al. (2013) Deficit in long-term synaptic plasticity is rescued by a computationally predicted stimulus protocol. J Neurosci 33: 6944-6949.
25. Jia J, Zhu F, Ma X, Cao Z, Li Y, et al. (2009) Mechanisms of drug combinations: interaction and network perspectives. Nat Rev Drug Discov 8: 111-128.
26. Song H, Smolen P, Av-Ron E, Baxter DA, Byrne JH, (2007) Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins. Biophys J 92: 3407-3424.
27. Mohamed HA, Yao W, Fioravante D, Smolen PD, Byrne JH, (2005) cAMP-response elements in Aplysia creb1, creb2, and Ap-uch promoters: implications for feedback loops modulating long term memory. J Biol Chem 280: 27035-27043.
28. Mangan S, Alon U, (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 100: 11980-11985.
29. Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, et al. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci USA 101: 5934-5939.
30. Coultrap SJ, Bayer KU, (2012) CaMKII regulation in information processing and storage. Trends Neurosci 35: 607-618.
31. Pickin KA, Chaudhury S, Dancy BC, Gray JJ, Cole PA, (2008) Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling. J Am Chem Soc 130: 5667-5669.
32. Goldoni M, Taqliaferri S, (2011) Dose-response or dose-effect curves in in vitro experiments and their use to study effect of neurotoxicants. Methods Mol Biol 785: 415-434.
33. Loewe S, (1953) The problem of synergism and antagonism of combined drugs. Arzneim-Forsch 3: 285-290.
34. Novick SJ, (2013) A simple test for synergy for small number of combinations. Stat Med Aug 13: 5145-55 doi:10.1002/sim.5905.
35. Bliss CL, (1939) The toxicity of poisons applied jointly. Ann Appl Biol 26: 585-615.
36. Yan H, Zhang B, Li S, Zhao Q, (2010) A formal model for analyzing drug combination effects and its application in TNF-α-induced NFκB pathway. BMC Syst Biol 4: 50 doi:10.1186/1752-0509-4-50.
37. Chou T-C, Talalay P, (1983) Analysis of combined drug effects: a new look at a very old problem. Trends Pharmacol Sci 4: 450-454.
38. Peterson JJ, Novick SJ, (2007) Nonlinear blending: a useful general concept for the assessment of combination drug synergy. J Recept Signal Transduct Res 27: 125-146.
39. Montarolo PG, Goelet P, Castellucci VF, Morgan J, Kandel ER, Schacher S, (1986) A critical period for macromolecular synthesis in long-term heterosynaptic facilitation in Aplysia. Science 234: 1249-1254.
40. Prill RJ, Iglesias PA, Levchenko A, (2005) Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 3 (11) (): e343.
41. Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine A, et al. (2004) Dynamics of the p53-Mdm2 feedback loop in individual cells. Nature Gen 36: 147-150.
42. Pratilas CA, Solit DB, (2010) Targeting the mitogen-activated protein kinase pathway: physiological feedback and drug response. Clin Cancer Res 16: 3329-3334.
43. Fritsche-Guenther R, Witzel F, Sieber A, Herr R, Schmidt N, et al. (2011) Strong negative feedback from Erk to Raf confers robustness to MAPK signaling. Mol Systems Biol 7: 489-502.
44. Alarcon JM, Malleret G, Touzani K, Vronskaya S, Ishii S, et al. (2004) Chromatin acetylation, memory, and LTP are impaired in CBP+/- mice: a model for the cognitive deficit in Rubinstein-Taybi syndrome and its amelioration. Neuron 42: 947-959.
45. Guilding C, McNair K, Stone TW, Morris BJ, (2007) Restored plasticity in a mouse model of neurofibromatosis type 1 via inhibition of hyperactive ERK and CREB. Eur J Neurosci 25: 99-105.
46. Ma'ayan A, Jenkins SL, Neves S, Hasseldine A, Grace E, et al. (2005) Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science 309: 1078-1083.
47. Alvarez XA, Cacabelos R, Sampedro C, Couceiro V, Aleixandre M, et al. (2011) Combinational treatment in Alzheimer's disease: results of a randomized, controlled trail with cerebroysin and donepezil. Curr Alzheimer Res 8: 583-591.
48. Bijnsdorp IV, Giovannetti E, Peters GJ, (2011) Analysis of drug interactions. Methods Mol Biol 731: 421-434.
49. Chauhan NB, Gatto R, (2010) Synergistic benefits of erythropoietin and simvastatin after traumatic brain injury. Brain Res 1360: 177-192.
50. Chou TC, (2006) Theoretical basis, experimental design, and computerized simulation of synergism and antagonism in drug combination studies. Pharmacol Rev 56: 621-668.
51. Marchetti C, Tafi E, Middei S, Rubinacci MA, Restivo L, et al. (2010) Synaptic adaptations of CA1 pyramidal neurons induced by highly effective combination antidepressant therapy. Biol Psychiatry 67: 146-154.
52. Marcus MM, Jardemark K, Malmerfelt A, Gertow J, Kondradsson-Geuden A, et al. (2012) Augmentation by escitalopram, but not citalopram or R-citalopream, of the effects of low-dose risperidone: behavioral, biochemical, and electrophysiological evidence. Synapse 66: 277-290.
53. Stiborova M, Eckschlager T, Poljakova J, Hrabeta J, Adam V, et al. (2012) The synergistic effects of DNA-targeted chemotherapeautics and histone deacetylase inhibitors as therapeutic strategies for cancer treatment. Curr Med Chem 19: 4218-4238.
54. Tamma PD, Cosgrove SE, Maragakis LL, (2012) Combination therapy for treatment of infections with gram-negative bacteria. Clin Microbiol Rev 25: 450-470.
55. Geary N, (2013) Understanding synergy. Am J Physiol Endocrinol Metab 304: E237-E253.
56. Tallarida RJ, (2012) Revisiting the isobole and related quantitative methods for assessing drug synergism. J Pharmacol Exp Ther 342: 2-8.
57. Axelrod M, Gordon VL, Conaway M, Tarcsafalvi A, Neitzke DJ, et al. (2009) Combinatorial drug screening identifies compensatory pathway interactions and adaptive resistance mechanisms. Oncotarget 4: 622-635.
58. Tyson JJ, Novak B, (2010) Functional motifs in biochemical reaction networks. Annu Rev Phys Chem 61: 219-240.