Combined logical and data-driven models for linking signalling pathways to cellular response

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Melas, Ioannis N ^a   Mitsos, Alexander ^b   Messinis, Dimitris E ^a   Weiss, Thomas S ^c   Alexopoulos, Leonidas G ^a  

^a NATIONAL TECHNICAL UNIVERSITY OF ATHENS   (Greece)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c UNIVERSITY HOSPITAL REGENSBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CALIBRATION; FACTUAL DATABASE; HUMAN; LOGIC; REPRODUCIBILITY; SIGNAL TRANSDUCTION; STATISTICAL MODEL; TUMOR CELL LINE;

CALIBRATION; CELL LINE, TUMOR; DATABASES, FACTUAL; HUMANS; LINEAR MODELS; LOGIC; MODELS, BIOLOGICAL; REPRODUCIBILITY OF RESULTS; SIGNAL TRANSDUCTION;

EID: 79959816776     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-107     Document Type: Article

References (50)

1. Downward J. The ins and outs of signalling. Nature 2001, 411:759-762. 10.1038/35081138, 11459043.
2. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7.
3. Friedman A, Perrimon N. Genetic screening for signal transduction in the era of network biology. Cell 2007, 128:225-231. 10.1016/j.cell.2007.01.007, 17254958.
4. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537. 10.1126/science.286.5439.531, 10521349.
5. Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 2003, 422:198-207. 10.1038/nature01511, 12634793.
6. Pandey A, Mann M. Proteomics to study genes and genomes. Nature 2000, 405:837-846. 10.1038/35015709, 10866210.
7. Deisboeck TS. Personalizing medicine: a systems biology perspective. Mol Syst Biol 2009, 5.
8. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA. E-CELL: software environment for whole-cell simulation. Bioinformatics 1999, 15:72-84. 10.1093/bioinformatics/15.1.72, 10068694.
9. Janes KA, Lauffenburger DA. A biological approach to computational models of proteomic networks. Curr Opin Chem Biol 2006, 10:73-80. 10.1016/j.cbpa.2005.12.016, 16406679.
10. Ideker T, Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 2003, 21:255-262. 10.1016/S0167-7799(03)00115-X, 12788545.
11. Cosgrove BD, Alexopoulos LG, Saez-Rodriguez J, Griffith LG, Lauffenburger DA. A multipathway phosphoproteomic signalling network model of idiosyncratic drug- and inflammatory cytokine-induced toxicity in human hepatocytes. Conf Proc IEEE Eng Med Biol Soc 2009, 2009:5452-5455.
12. Janes KA, Yaffe MB. Data-driven modelling of signal-transduction networks. Nat Rev Mol Cell Bio 2006, 7:820-828.
13. Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK. Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signalling between normal and transformed hepatocytes. Mol Cell Proteomics 2010, 9:1849-1865. 10.1074/mcp.M110.000406, 2938121, 20460255.
14. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP. Causal Protein-Signalling Networks Derived from Multiparameter Single-Cell Data. Science 2005, 308:523-529. 10.1126/science.1105809, 15845847.
15. Aldridge BB, Burke JM, Lauffenburger DA, Sorger PK. Physicochemical modelling of cell signalling pathways. Nat Cell Biol 2006, 8:1195-1203. 10.1038/ncb1497, 17060902.
16. Kholodenko BN, Demin OV, Moehren G, Hoek JB. Quantification of short term signalling by the epidermal growth factor receptor. Journal of Biological Chemistry 1999, 274:30169-30181. 10.1074/jbc.274.42.30169, 10514507.
17. Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA. Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signalling. Plos Computational Biology 2009, 5.
18. Morris MK, Saez-Rodriguez J, Clarke DC, Sorger PK, Lauffenburger DA. Training signalling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput Biol 2011 2011, 7(3):e1001099.
19. Morris MK, Saez-Rodriguez J, Sorger PK, Lauffenburger DA. Logic-Based Models for the Analysis of Cell Signalling Networks. Biochemistry-Us 2010, 49:3216-3224.
20. Samaga R, Saez-Rodriguez J, Alexopoulos LG, Sorger PK, Klamt S. The Logic of EGFR/ErbB Signalling: Theoretical Properties and Analysis of High-Throughput Data. Plos Computational Biology 2009, 5.
21. Schlatter R, Schmich K, Avalos Vizcarra I, Scheurich P, Sauter T, Borner C, Ederer M, Merfort I, Sawodny O. ON/OFF and Beyond - A Boolean Model of Apoptosis. PLoS Comput Biol 2009, 5:e1000595. 10.1371/journal.pcbi.1000595, 2781112, 20011108.
22. Kaufman M, Andris F, Leo O. A logical analysis of T cell activation and anergy. P Natl Acad Sci USA 1999, 96:3894-3899.
23. Mitsos A, Melas IN, Siminelakis P, Chairakaki AD, Saez-Rodriguez J, Alexopoulos LG. Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data. PLoS Comput Biol 2009, 5:e1000591. 10.1371/journal.pcbi.1000591, 2776985, 19997482.
24. Saez-Rodriguez J, Alexopoulos LG, Epperlein J, Samaga R, Lauffenburger DA, Klamt S, Sorger PK. Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol 2009, 5:331. 2824489, 19953085.
25. Gaudet S, Janes KA, Albeck JG, Pace EA, Lauffenburger DA, Sorger PK. A compendium of signals and responses triggered by prodeath and prosurvival cytokines. Mol Cell Proteomics 2005, 4:1569-1590. Epub 2005 Jul 1518, 10.1074/mcp.M500158-MCP200, 16030008.
26. Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB. A Systems Model of Signalling Identifies a Molecular Basis Set for Cytokine-Induced Apoptosis. Science 2005, 310:1646-1653. 10.1126/science.1116598, 16339439.
27. Peng SC, Wong DS, Tung KC, Chen YY, Chao CC, Peng CH, Chuang YJ, Tang CY. Computational modeling with forward and reverse engineering links signalling network and genomic regulatory responses: NF-kappaB signalling-induced gene expression responses in inflammation. BMC Bioinformatics 2010, 11:308. 10.1186/1471-2105-11-308, 2889938, 20529327.
28. El-Serag HB, Rudolph L. Hepatocellular carcinoma: Epidemiology and molecular carcinogenesis. Gastroenterology 2007, 132:2557-2576. 10.1053/j.gastro.2007.04.061, 17570226.
29. Parkin DM, Bray F, Ferlay J, Pisani P. Global cancer statistics, 2002. Ca-Cancer J Clin 2005, 55:74-108. 10.3322/canjclin.55.2.74, 15761078.
30. Nakabayashi H, Taketa K, Miyano K, Yamane T, Sato J. Growth of Human Hepatoma Cell Lines with Differentiated Functions in Chemically Defined Medium. Cancer Research 1982, 42:3858-3863.
31. Michael MD, Kulkarni RN, Postic C, Previs SF, Shulman GI, Magnuson MA, Kahn CR. Loss of Insulin Signalling in Hepatocytes Leads to Severe Insulin Resistance and Progressive Hepatic Dysfunction. Molecular Cell 2000, 6:87-97.
32. Xia WL, Mullin RJ, Keith BR, Liu LH, Ma H, Rusnak DW, Owens G, Alligood KJ, Spector NL. Anti-tumor activity of GW572016: a dual tyrosine kinase inhibitor blocks EGF activation of EGFR/erbB2 and downstream Erk1/2 and AKT pathways. Oncogene 2002, 21:6255-6263. 10.1038/sj.onc.1205794, 12214266.
33. Iyer R, Bharthuar A. A review of erlotinib - an oral, selective epidermal growth factor receptor tyrosine kinase inhibitor. Expert Opin Pharmaco 2010, 11:311-320.
34. Wood ER, Truesdale AT, McDonald OB, Yuan D, Hassell A, Dickerson SH, Ellis B, Pennisi C, Horne E, Lackey K, Alligood KJ, Rusnak DW, Gilmer TM, Shewchuk L. A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): Relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Research 2004, 64:6652-6659. 10.1158/0008-5472.CAN-04-1168, 15374980.
35. Saez-Rodriguez J, Goldsipe A, Muhlich J, Alexopoulos LG, Millard B, Lauffenburger DA, Sorger PK. Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics 2008, 24:840-847. 10.1093/bioinformatics/btn018, 2617752, 18218655.
36. Brooke A, Kendrick D, Meeraus A. GAMS: User's Guide 1988, Redwood City, California: The Scientific Press.
37. Karaman MW, Herrgard S, Treiber DK, Gallant P, Atteridge CE, Campbell BT, Chan KW, Ciceri P, Davis MI, Edeen PT, Faraoni R, Floyd M, Hunt JP, Lockhart DJ, Milanov ZV, Morrison MJ, Pallares G, Patel HK, Pritchard S, Wodicka LM, Zarrinkar PP. A quantitative analysis of kinase inhibitor selectivity. Nat Biotech 2008, 26:127-132.
38. Hanada T, Yoshimura A. Regulation of cytokine signalling and inflammation. Cytokine Growth Factor Rev 2002, 13:413-421. 10.1016/S1359-6101(02)00026-6, 12220554.
39. Toffanin S, Friedman SL, Llovet JM. Obesity, Inflammatory Signalling, and Hepatocellular Carcinoma An Enlarging Link. Cancer Cell 2010, 17:115-117. 10.1016/j.ccr.2010.01.018, 20159605.
40. Firestein GS. Evolving concepts of rheumatoid arthritis. Nature 2003, 423:356-361. 10.1038/nature01661, 12748655.
41. Birrell MA, Hardaker E, Wong S, McCluskie K, Catley M, De Alba J, Newton R, Haj-Yahia S, Pun KT, Watts CJ, Shaw RJ, Savage TJ, Belvisi MG. I{kappa}-B Kinase-2 Inhibitor Blocks Inflammation in Human Airway Smooth Muscle and a Rat Model of Asthma. Am J Respir Crit Care Med 2005, 172:962-971. 10.1164/rccm.200412-1647OC, 16002568.
42. Yoshimura A. Signal transduction of inflammatory cytokines and tumor development. Cancer Science 2006, 97:439-447. 10.1111/j.1349-7006.2006.00197.x, 16734720.
43. Grivennikov SI, Greten FR, Karin M. Immunity, Inflammation, and Cancer. Cell 140:883-899.
44. Kortylewski M, Kujawski M, Wang T, Wei S, Zhang S, Pilon-Thomas S, Niu G, Kay H, Mule J, Kerr WG, Jove R, Pardoll D, Yu H. Inhibiting Stat3 signalling in the hematopoietic system elicits multicomponent antitumor immunity. Nat Med 2005, 11:1314-1321. Epub 2005 Nov 1320, 10.1038/nm1325, 16288283.
45. Teicher BA. Transforming growth factor-beta and the immune response to malignant disease. Clin Cancer Res 2007, 13:6247-6251. 10.1158/1078-0432.CCR-07-1654, 17975134.
46. Wang T, Niu G, Kortylewski M, Burdelya L, Shain K, Zhang S, Bhattacharya R, Gabrilovich D, Heller R, Coppola D, Dalton W, Jove R, Pardoll D, Yu H. Regulation of the innate and adaptive immune responses by Stat-3 signalling in tumor cells. Nat Med 2004, 10:48-54. Epub 2003 Dec 2021, 10.1038/nm976, 14702634.
47. Taniguchi CM, Winnay J, Kondo T, Bronson RT, Guimaraes AR, Alemán JO, Luo J, Stephanopoulos G, Weissleder R, Cantley LC, Kahn CR. The Phosphoinositide 3-Kinase Regulatory Subunit p85α Can Exert Tumor Suppressor Properties through Negative Regulation of Growth Factor Signalling. Cancer Research 2010, 70:5305-5315. 10.1158/0008-5472.CAN-09-3399, 20530665.
48. Hanahan D, Weinberg RA. The Hallmarks of Cancer. Cell 2000, 100:57-70. 10.1016/S0092-8674(00)81683-9, 10647931.
49. Thomas SW, Sascha P, Irmgard S, Karl-Walter J, Wolfgang ET. Cellular damage to human hepatocytes through repeated application of 5-aminolevulinic acid. Journal of hepatology 2003, 38:476-482.
50. Thasler WE, Weiss TS, Schillhorn K, Stoll PT, Irrgang B, Jauch KW. Charitable State-Controlled Foundation Human Tissue and Cell Research: Ethic and Legal Aspects in the Supply of Surgically Removed Human Tissue For Research in the Academic and Commercial Sector in Germany. Cell and Tissue Banking 2003, 4:49-56. 10.1023/A:1026392429112, 15256870.