Towards a systems biology approach of G protein-coupled receptor signalling: Challenges and expectations

Comptes Rendus - Biologies

Volumn 332, Issue 11, 2009, Pages 947-957

  Heitzler, Domitille ^a,b,c,d   Crépieux, Pascale ^a,b,c,d   Poupon, Anne ^a,b,c,d   Clément, Frédérique ^e   Fages, François ^e   Reiter, Eric ^a,b,c,d  

^a UMR85 PHYSIOLOGIE DE LA REPRODUCTION ET DES COMPORTEMENTS   (France)

^b CNRS   (France)

^c UNIVERSITÉ DE TOURS   (France)

^d Haras Nationaux   (France)

^e INRIA   (France)

Author keywords

Bioinformatics; GPCR; Modelling; Pharmacology; Signalling; Systems biology

Indexed keywords

BETA ARRESTIN; CARVEDILOL; G PROTEIN COUPLED RECEPTOR;

BIOINFORMATICS; DRUG; MODELING; PHYSIOLOGY;

BIOINFORMATICS; DRUG PROTEIN BINDING; ENZYME ACTIVATION; HEART FAILURE; HUMAN; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PROTEIN MICROARRAY; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; RECEPTOR BINDING; RECEPTOR SENSITIVITY; SHORT SURVEY; SIGNAL TRANSDUCTION;

ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DRUG DISCOVERY; FLUORESCENCE RESONANCE ENERGY TRANSFER; HETEROTRIMERIC GTP-BINDING PROTEINS; INTERDISCIPLINARY COMMUNICATION; LIGANDS; MODELS, BIOLOGICAL; PROTEOMICS; RECEPTORS, G-PROTEIN-COUPLED; RESEARCH; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 70449522311     PISSN: 16310691     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.crvi.2009.09.002     Document Type: Short Survey

References (65)

1. Preisinger C., von Kriegsheim A., Matallanas D., and Kolch W. Proteomics and phosphoproteomics for the mapping of cellular signalling networks. Proteomics 8 (2008) 4402-4415
2. Kell D.B. Theodor Bucher Lecture: Metabolomics, modelling and machine learning in systems biology - Towards an understanding of the languages of cells. FEBS J. 273 (2006) 873-894 Delivered on 3 July 2005 at the 30th FEBS Congress and the 9th IUBMB Conference in Budapest
3. Ma P., and Zemmel R. Value of novelty?. Nat. Rev. Drug Discov. 1 (2002) 571-572
4. Luttrell L.M. Transmembrane signaling by G protein-coupled receptors. Methods Mol. Biol. 332 (2006) 3-49
5. Lefkowitz R.J., Pierce K.L., and Luttrell L.M. Dancing with different partners: Protein kinase a phosphorylation of seven membrane-spanning receptors regulates their G protein-coupling specificity. Mol. Pharmacol. 62 (2002) 971-974
6. Bockaert J., Dumuis A., Fagni L., and Marin P. GPCR-GIP networks: A first step in the discovery of new therapeutic drugs?. Curr. Opin. Drug Discov. Devel. 7 (2004) 649-657
7. Lefkowitz R.J., and Shenoy S.K. Transduction of receptor signals by beta-arrestins. Science 308 (2005) 512-517
8. Lefkowitz R.J. G protein-coupled receptors. III. New roles for receptor kinases and beta-arrestins in receptor signaling and desensitization. J. Biol. Chem. 273 (1998) 18677-18680
9. Witherow D.S., Garrison T.R., Miller W.E., and Lefkowitz R.J. Beta-arrestin inhibits NF-kappaB activity by means of its interaction with the NF-kappaB inhibitor IkappaBalpha. Proc. Natl. Acad. Sci. USA 101 (2004) 8603-8607
10. Barnes W.G., Reiter E., Violin J.D., Ren X.R., Milligan G., and Lefkowitz R.J. {beta}-Arrestin 1 and G{alpha}q/11 coordinately activate RhoA and stress fiber formation following receptor stimulation. J. Biol. Chem. 280 (2005) 8041-8050
11. Beaulieu J.M., Sotnikova T.D., Marion S., Lefkowitz R.J., Gainetdinov R.R., and Caron M.G. An Akt/beta-arrestin 2/PP2A signaling complex mediates dopaminergic neurotransmission and behavior. Cell 122 (2005) 261-273
12. Hunton D.L., Barnes W.G., Kim J., Ren X.R., Violin J.D., Reiter E., Milligan G., Patel D.D., and Lefkowitz R.J. Beta-arrestin 2-dependent angiotensin II type 1A receptor-mediated pathway of chemotaxis. Mol. Pharmacol. 67 (2005) 1229-1236
13. Reiter E., and Lefkowitz R.J. GRKs and beta-arrestins: Roles in receptor silencing, trafficking and signaling. Trends Endocrinol. Metab. 17 (2006) 159-165
14. Xiao K., McClatchy D.B., Shukla A.K., Zhao Y., Chen M., Shenoy S.K., Yates III J.R., and Lefkowitz R.J. Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proc. Natl. Acad. Sci. USA 104 (2007) 12011-12016
15. Penela P., Ribas C., and Mayor Jr. F. Mechanisms of regulation of the expression and function of G protein-coupled receptor kinases. Cell. Signal. 15 (2003) 973-981
16. Lorenz K., Lohse M.J., and Quitterer U. Protein kinase C switches the Raf kinase inhibitor from Raf-1 to GRK-2. Nature 426 (2003) 574-579
17. Liu S., Premont R.T., Kontos C.D., Zhu S., and Rockey D.C. A crucial role for GRK2 in regulation of endothelial cell nitric oxide synthase function in portal hypertension. Nat. Med. 11 (2005) 952-958
18. Jimenez-Sainz M.C., Murga C., Kavelaars A., Jurado-Pueyo M., Kraastak B.F., Heijnen C.J., Mayor Jr. F., and Aragay A.M. G protein-coupled receptor kinase 2 negatively regulates chemokine signaling at a level downstream from G protein subunits. Mol. Biol. Cell 17 (2006) 25-31
19. Komarova N.L., Zou X., Nie Q., and Bardwell L. A theoretical framework for specificity in cell signaling. Mol. Syst. Biol. 1 (2005) 2005.0023
20. McClean M.N., Mody A., Broach J.R., and Ramanathan S. Cross-talk and decision making in MAP kinase pathways. Nat. Genet. 39 (2007) 409-414
21. Behar M., Hao N., Dohlman H.G., and Elston T.C. Dose-to-duration encoding and signaling beyond saturation in intracellular signaling networks. PLoS Comput. Biol. 4 (2008) e1000197
22. Ren X.R., Reiter E., Ahn S., Kim J., Chen W., and Lefkowitz R.J. Different G protein-coupled receptor kinases govern G protein and {beta}-arrestin-mediated signaling of V2 vasopressin receptor. Proc. Natl. Acad. Sci. USA 102 (2005) 1448-1453
23. Shenoy S.K., Drake M.T., Nelson C.D., Houtz D.A., Xiao K., Madabushi S., Reiter E., Premont R.T., Lichtarge O., and Lefkowitz R.J. Beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor. J. Biol. Chem. 281 (2006) 1261-1273
24. Ahn S., Shenoy S.K., Wei H., and Lefkowitz R.J. Differential kinetic and spatial patterns of beta-arrestin and G protein-mediated ERK activation by the angiotensin II receptor. J. Biol. Chem. 279 (2004) 35518-35525
25. Wei H., Ahn S., Shenoy S.K., Karnik S.S., Hunyady L., Luttrell L.M., and Lefkowitz R.J. Independent beta-arrestin 2 and G protein-mediated pathways for angiotensin II activation of extracellular signal-regulated kinases 1 and 2. Proc. Natl. Acad. Sci. USA 100 (2003) 10782-10787
26. Kara E., Crepieux P., Gauthier C., Martinat N., Piketty V., Guillou F., and Reiter E. A phosphorylation cluster of five serine and threonine residues in the C-terminus of the follicle-stimulating hormone receptor is important for desensitization but not for beta-arrestin-mediated ERK activation. Mol. Endocrinol. 20 (2006) 3014-3026
27. Violin J.D., and Lefkowitz R.J. Beta-arrestin-biased ligands at seven-transmembrane receptors. Trends Pharmacol. Sci. 28 (2007) 416-422
28. Kenakin T. Collateral efficacy in drug discovery: Taking advantage of the good (allosteric) nature of 7TM receptors. Trends Pharmacol. Sci. 28 (2007) 407-415
29. Gesty-Palmer D., Chen M., Reiter E., Ahn S., Nelson C.D., Wang S., Eckhardt A.E., Cowan C.L., Spurney R.F., Luttrell L.M., and Lefkowitz R.J. Distinct beta-arrestin- and G protein-dependent pathways for parathyroid hormone receptor-stimulated ERK1/2 activation. J. Biol. Chem. 281 (2006) 10856-10864
30. Drake M.T., Violin J.D., Whalen E.J., Wisler J.W., Shenoy S.K., and Lefkowitz R.J. Beta-arrestin-biased agonism at the beta2-adrenergic receptor. J. Biol. Chem. 283 (2008) 5669-5676
31. Wisler J.W., DeWire S.M., Whalen E.J., Violin J.D., Drake M.T., Ahn S., Shenoy S.K., and Lefkowitz R.J. A unique mechanism of beta-blocker action: Carvedilol stimulates beta-arrestin signaling. Proc. Natl. Acad. Sci. USA 104 (2007) 16657-16662
32. Hao N., Behar M., Elston T.C., and Dohlman H.G. Systems biology analysis of G protein and MAP kinase signaling in yeast. Oncogene 26 (2007) 3254-3266
33. Hao N., Behar M., Parnell S.C., Torres M.P., Borchers C.H., Elston T.C., and Dohlman H.G. A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway. Curr. Biol. 17 (2007) 659-667
34. Linderman J.J. Modeling of G-protein-coupled receptor signaling pathways. J. Biol. Chem. 284 (2009) 5427-5431
35. Von Bertalanffy L. The theory of open systems in physics and biology. Science 111 (1950) 23-29
36. Stelzl U., Worm U., Lalowski M., Haenig C., Brembeck F.H., Goehler H., Stroedicke M., Zenkner M., Schoenherr A., Koeppen S., Timm J., Mintzlaff S., Abraham C., Bock N., Kietzmann S., Goedde A., Toksoz E., Droege A., Krobitsch S., Korn B., Birchmeier W., Lehrach H., and Wanker E.E. A human protein-protein interaction network: A resource for annotating the proteome. Cell 122 (2005) 957-968
37. Linding R., Jensen L.J., Ostheimer G.J., van Vugt M.A., Jorgensen C., Miron I.M., Diella F., Colwill K., Taylor L., Elder K., Metalnikov P., Nguyen V., Pasculescu A., Jin J., Park J.G., Samson L.D., Woodgett J.R., Russell R.B., Bork P., Yaffe M.B., and Pawson T. Systematic discovery of in vivo phosphorylation networks. Cell 129 (2007) 1415-1426
38. Witze E.S., Old W.M., Resing K.A., and Ahn N.G. Mapping protein post-translational modifications with mass spectrometry. Nat. Methods 4 (2007) 798-806
39. Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., and Mann M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127 (2006) 635-648
40. Spurrier B., Ramalingam S., and Nishizuka S. Reverse-phase protein lysate microarrays for cell signaling analysis. Nat. Protoc. 3 (2008) 1796-1808
41. Chan S.M., Ermann J., Su L., Fathman C.G., and Utz P.J. Protein microarrays for multiplex analysis of signal transduction pathways. Nat. Med. 10 (2004) 1390-1396
42. Gembitsky D.S., Lawlor K., Jacovina A., Yaneva M., and Tempst P. A prototype antibody microarray platform to monitor changes in protein tyrosine phosphorylation. Mol. Cell. Proteomics 3 (2004) 1102-1118
43. Sheehan K.M., Calvert V.S., Kay E.W., Lu Y., Fishman D., Espina V., Aquino J., Speer R., Araujo R., Mills G.B., Liotta L.A., Petricoin III E.F., and Wulfkuhle J.D. Use of reverse phase protein microarrays and reference standard development for molecular network analysis of metastatic ovarian carcinoma. Mol. Cell. Proteomics 4 (2005) 346-355
44. Lohse M.J., Nikolaev V.O., Hein P., Hoffmann C., Vilardaga J.P., and Bunemann M. Optical techniques to analyze real-time activation and signaling of G-protein-coupled receptors. Trends Pharmacol. Sci. 29 (2008) 159-165
45. Allen M.D., DiPilato L.M., Ananthanarayanan B., Newman R.H., Ni Q., and Zhang J. Dynamic visualization of signaling activities in living cells. Sci. Signal. 1 (2008) pt6
46. Giepmans B.N., Adams S.R., Ellisman M.H., and Tsien R.Y. The fluorescent toolbox for assessing protein location and function. Science 312 (2006) 217-224
47. Charest P.G., Terrillon S., and Bouvier M. Monitoring agonist-promoted conformational changes of beta-arrestin in living cells by intramolecular BRET. EMBO Rep. 6 (2005) 334-340
48. Gales C., Rebois R.V., Hogue M., Trieu P., Breit A., Hebert T.E., and Bouvier M. Real-time monitoring of receptor and G-protein interactions in living cells. Nat. Methods 2 (2005) 177-184
49. Azizi F., and Mastrangelo C.H. Generation of dynamic chemical signals with pulse code modulators. Lab Chip 8 (2008) 907-912
50. Hung P.J., Lee P.J., Sabounchi P., Lin R., and Lee L.P. Continuous perfusion microfluidic cell culture array for high-throughput cell-based assays. Biotechnol. Bioeng. 89 (2005) 1-8
51. Erfle H., Neumann B., Rogers P., Bulkescher J., Ellenberg J., and Pepperkok R. Work flow for multiplexing siRNA assays by solid-phase reverse transfection in multiwell plates. J. Biomol. Screen 13 (2008) 575-580
52. Starkuviene V., Pepperkok R., and Erfle H. Transfected cell microarrays: An efficient tool for high-throughput functional analysis. Expert Rev. Proteomics 4 (2007) 479-489
53. Castel D., Debily M.A., Pitaval A., and Gidrol X. Cell microarray for functional exploration of genomes. Methods Mol. Biol. 381 (2007) 375-384
54. Nelander S., Wang W., Nilsson B., She Q.B., Pratilas C., Rosen N., Gennemark P., and Sander C. Models from experiments: Combinatorial drug perturbations of cancer cells. Mol. Syst. Biol. 4 (2008) 216
55. Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Gilles E.D., Ginkel M., Gor Goryanin II V., Hedley W.J., Hodgman T.C., Hofmeyr J.H., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novere N., Loew L.M., Lucio D., Mendes P., Minch E., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., and Wang J. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19 (2003) 524-531
56. Kitano H., Funahashi A., Matsuoka Y., and Oda K. Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 23 (2005) 961-966
57. A. Funahashi, Y. Matsuoka, A. Jouraku, M. Morohashi, N. Kikuchi, H. Kitano, CellDesigner 3.5: A versatile modeling tool for biochemical networks, in: Proceedings of the IEEE, 2008, pp. 1254-1265
58. Calzone L., Fages F., and Soliman S. BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22 (2006) 1805-1807
59. Fages F., and Soliman S. From reaction models to influence graphs and back: A theorem. Formal Methods in Systems Biology. LNBI vol. 5054 (2008), Springer-Verlag 90-102
60. Fages F., and Soliman S. Formal cell biology in BIOCHAM. International School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology, Bertinoro, Italy. LNCS vol. 5016 (2008), Springer-Verlag 54-80
61. Gilbert D., Fuss H., Gu X., Orton R., Robinson S., Vyshemirsky V., Kurth M.J., Downes C.S., and Dubitzky W. Computational methodologies for modelling, analysis and simulation of signalling networks. Brief Bioinform. 7 (2006) 339-353
62. Orton R.J., Sturm O.E., Vyshemirsky V., Calder M., Gilbert D.R., and Kolch W. Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. Biochem. J. 392 (2005) 249-261
63. Rizk A., Batt G., Fages F., and Soliman S. On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology. Computational Methods in Systems Biology CMSB'08. LNBI vol. 5307 (2008), Springer-Verlag 251-268
64. Hansen N., and Ostermeier A. Completely derandomized self-adaptation in evolution strategies. Evol. Comput. 9 (2001) 159-195
65. Rizk A., Batt G., Fages F., and Soliman S. A general computational method for robustness analysis with applications to synthetic gene networks. 17th Annual International Conference on Intelligent Systems for Molecular Biology. Bioinformatics 25 (2009) 169-178