A Systems Biology Strategy for Predicting Similarities and Differences of Drug Effects: Evidence for Drug-specific Modulation of Inflammation in Atherosclerosis

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Kleemann, Robert ^a   Bureeva, Svetlana ^b   Perlina, Ally ^b   Kaput, Jim ^c,d   Verschuren, Lars ^a   Wielinga, Peter Y ^a   Hurt Camejo, Eva ^e   Nikolsky, Yuri ^b   van Ommen, Ben ^a   Kooistra, Teake ^a  

^a TNO   (Netherlands)

^b GeneGo Inc   (United States)

^c NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^d EPFL   (Switzerland)

^e ASTRAZENECA R AND D   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

TRIFLUORO;

ANTIINFLAMMATORY AGENT; CARDIOVASCULAR AGENT; FENOFIBRATE; FLUORINATED HYDROCARBON; FLUOROBENZENE; N (2,2,2 TRIFLUOROETHYL) N [4 (2,2,2 TRIFLUORO 1 HYDROXY 1 TRIFLUOROMETHYLETHYL)PHENYL]BENZENESULFONAMIDE; PYRIMIDINE DERIVATIVE; ROSUVASTATIN; SULFONAMIDE; TO-901317;

ANIMAL; ARTICLE; ATHEROSCLEROSIS; BIOLOGICAL MODEL; DRUG DESIGN; DRUG EFFECT; GENE EXPRESSION REGULATION; HUMAN; METHODOLOGY; MICROARRAY ANALYSIS; MOUSE; REGULATORY SEQUENCE; STRUCTURE ACTIVITY RELATION; SYSTEMS BIOLOGY;

ANIMALS; ANTI-INFLAMMATORY AGENTS; ATHEROSCLEROSIS; CARDIOVASCULAR AGENTS; DRUG DESIGN; FENOFIBRATE; FLUOROBENZENES; GENE EXPRESSION REGULATION; HUMANS; HYDROCARBONS, FLUORINATED; MICE; MICROARRAY ANALYSIS; MODELS, BIOLOGICAL; PYRIMIDINES; REGULATORY ELEMENTS, TRANSCRIPTIONAL; STRUCTURE-ACTIVITY RELATIONSHIP; SULFONAMIDES; SYSTEMS BIOLOGY;

EID: 80051595500     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-125     Document Type: Article

References (38)

1. Ashburn TT, Thor KB. Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 2004, 3:673-683. 10.1038/nrd1468, 15286734.
2. Riggs BL, Hartmann LC. Selective estrogen-receptor modulators -- mechanisms of action and application to clinical practice. N Engl J Med 2003, 348:618-629. 10.1056/NEJMra022219, 12584371.
3. Ericson E, Gebbia M, Heisler LE, Wildenhain J, Tyers M, Giaever G, Nislow C. Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast. PLoS Genet 2008, 4:e1000151. 10.1371/journal.pgen.1000151, 2483942, 18688276.
4. Strony J, Hoffman R, Hanson M, Veltri E. Tolerability and effects on lipids of ezetimibe coadministered with pravastatin or simvastatin for twelve months: results from two open-label extension studies in hypercholesterolemic patients. Clin Ther 2008, 30:2280-2297. 10.1016/j.clinthera.2008.12.008, 19167588.
5. Howes LG, Kostner K. The withdrawal of torcetrapib from drug development: implications for the future of drugs that alter HDL metabolism. Expert Opin Investig Drugs 2007, 16:1509-1516. 10.1517/13543784.16.10.1509, 17922616.
6. Ekins S, Andreyev S, Ryabov A, Kirillov E, Rakhmatulin EA, Bugrim A, Nikolskaya T. Computational prediction of human drug metabolism. Expert Opin Drug Metab Toxicol 2005, 1:303-324. 10.1517/17425255.1.2.303, 16922645.
7. Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotechnol 2007, 25:197-206. 10.1038/nbt1284, 17287757.
8. Yusuf S, Reddy S, Ounpuu S, Anand S. Global burden of cardiovascular diseases: part I: general considerations, the epidemiologic transition, risk factors, and impact of urbanization. Circulation 2001, 104:2746-2753. 10.1161/hc4601.099487, 11723030.
9. Zadelaar S, Kleemann R, Verschuren L, de Vries-van der W, van der HJ, Princen HM, Kooistra T. Mouse models for atherosclerosis and pharmaceutical modifiers. Arterioscler Thromb Vasc Biol 2007, 27:1706-1721. 10.1161/ATVBAHA.107.142570, 17541027.
10. Zambon A, Gervois P, Pauletto P, Fruchart JC, Staels B. Modulation of hepatic inflammatory risk markers of cardiovascular diseases by PPAR-alpha activators: clinical and experimental evidence. Arterioscler Thromb Vasc Biol 2006, 26:977-986. 10.1161/01.ATV.0000204327.96431.9a, 16424352.
11. Kleemann R, Kooistra T. HMG-CoA reductase inhibitors: effects on chronic subacute inflammation and onset of atherosclerosis induced by dietary cholesterol. Curr Drug Targets Cardiovasc Haematol Disord 2005, 5:441-453. 10.2174/156800605774962077, 16503864.
12. Fievet C, Staels B. Liver × receptor modulators: effects on lipid metabolism and potential use in the treatment of atherosclerosis. Biochem Pharmacol 2009, 77:1316-1327. 10.1016/j.bcp.2008.11.026, 19101522.
13. Kleemann R, Princen HM, Emeis JJ, Jukema JW, Fontijn RD, Horrevoets AJ, Kooistra T, Havekes LM. Rosuvastatin reduces atherosclerosis development beyond and independent of its plasma cholesterol-lowering effect in APOE*3-Leiden transgenic mice: evidence for antiinflammatory effects of rosuvastatin. Circulation 2003, 108:1368-1374. 10.1161/01.CIR.0000086460.55494.AF, 12939225.
14. Kooistra T, Verschuren L, de Vries-van der W, Koenig W, Toet K, Princen HM, Kleemann R. Fenofibrate reduces atherogenesis in ApoE*3Leiden mice: evidence for multiple antiatherogenic effects besides lowering plasma cholesterol. Arterioscler Thromb Vasc Biol 2006, 26:2322-2330. 10.1161/01.ATV.0000238348.05028.14, 16873727.
15. Verschuren L, de Vries-van der W, Zadelaar S, Kleemann R, Kooistra T. LXR agonist suppresses atherosclerotic lesion growth and promotes lesion regression in apoE*3Leiden mice: time course and mechanisms. J Lipid Res 2009, 50:301-311.
16. Nikolsky Y, Kirillov E, Zuev R, Rakhmatulin E, Nikolskaya T. Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform. Methods Mol Biol 2009, 563:177-196. 10.1007/978-1-60761-175-2_10, 19597786.
17. Famer D, Crisby M. Rosuvastatin reduces caspase-3 activity and up-regulates alpha-secretase in human neuroblastoma SH-SY5Y cells exposed to A beta. Neurosci Lett 2004, 371:209-214. 10.1016/j.neulet.2004.08.069, 15519759.
18. el Kebbaj MH, Cherkaoui MM, Latruffe N. Effect of peroxisomes proliferators and hypolipemic agents on mitochondrial inner membrane linked D-3-hydroxybutyrate dehydrogenase (BDH). Biochem Mol Biol Int 1995, 35:65-77.
19. Gouedard C, Koum-Besson N, Barouki R, Morel Y. Opposite regulation of the human paraoxonase-1 gene PON-1 by fenofibrate and statins. Mol Pharmacol 2003, 63:945-956. 10.1124/mol.63.4.945, 12644596.
20. Lee JW, Bajwa PJ, Carson MJ, Jeske DR, Cong Y, Elson CO, Lytle C, Straus DS. Fenofibrate represses interleukin-17 and interferon-gamma expression and improves colitis in interleukin-10-deficient mice. Gastroenterology 2007, 133:108-123. 10.1053/j.gastro.2007.03.113, 17631136.
21. Karten B, Campenot RB, Vance DE, Vance JE. Expression of ABCG1, but not ABCA1, correlates with cholesterol release by cerebellar astroglia. J Biol Chem 2006, 281:4049-4057. 10.1074/jbc.M508915200, 16352604.
22. Wang J, Einarsson C, Murphy C, Parini P, Bjorkhem I, Gafvels M, Eggertsen G. Studies on LXR- and FXR-mediated effects on cholesterol homeostasis in normal and cholic acid-depleted mice. J Lipid Res 2006, 47:421-430.
23. Hu T, Foxworthy P, Siesky A, Ficorilli JV, Gao H, Li S, Christe M, Ryan T, Cao G, Eacho P, et al. Hepatic peroxisomal fatty acid beta-oxidation is regulated by liver × receptor alpha. Endocrinology 2005, 146:5380-5387. 10.1210/en.2005-0591, 16123164.
24. Castrillo A, Joseph SB, Marathe C, Mangelsdorf DJ, Tontonoz P. Liver × receptor-dependent repression of matrix metalloproteinase-9 expression in macrophages. J Biol Chem 2003, 278:10443-10449. 10.1074/jbc.M213071200, 12531895.
25. Xue Y, Chao E, Zuercher WJ, Willson TM, Collins JL, Redinbo MR. Crystal structure of the PXR-T1317 complex provides a scaffold to examine the potential for receptor antagonism. Bioorg Med Chem 2007, 15:2156-2166. 10.1016/j.bmc.2006.12.026, 1839856, 17215127.
26. Libby P, Ridker PM, Maseri A. Inflammation and atherosclerosis. Circulation 2002, 105:1135-1143. 10.1161/hc0902.104353, 11877368.
27. Kleemann R, Verschuren L, van Erk MJ, Nikolsky Y, Cnubben NH, Verheij ER, Smilde AK, Hendriks HF, Zadelaar S, Smith GJ, et al. Atherosclerosis and liver inflammation induced by increased dietary cholesterol intake: a combined transcriptomics and metabolomics analysis. Genome Biol 2007, 8:R200. 10.1186/gb-2007-8-9-r200, 2375038, 17892536.
28. Classen S, Muth C, bey-Pascher S, Eggle D, Beyer M, Mallmann MR, Rudlowski C, Zander T, Polcher M, Kuhn W, et al. Application of T cell-based transcriptomics to identify three candidate biomarkers for monitoring anti-TGFbetaR therapy. Pharmacogenet Genomics 2010, 20:147-156. 10.1097/FPC.0b013e328335731c, 20084050.
29. Chen L, Zhang J, Zhang Y, Wang Y, Wang B. Improvement of inflammatory responses associated with NF-kappa B pathway in kidneys from diabetic rats. Inflamm Res 2008, 57:199-204. 10.1007/s00011-006-6190-z, 18465086.
30. Okopien B, Krysiak R, Kowalski J, Madej A, Belowski D, Zielinski M, Herman ZS. Monocyte release of tumor necrosis factor-alpha and interleukin-1beta in primary type IIa and IIb dyslipidemic patients treated with statins or fibrates. J Cardiovasc Pharmacol 2005, 46:377-386. 10.1097/01.fjc.0000175455.46245.c8, 16116345.
31. Dai X, Ou X, Hao X, Cao D, Tang Y, Hu Y, Li X, Tang C. Effect of T0901317 on hepatic proinflammatory gene expression in apoE-/- mice fed a high-fat/high-cholesterol diet. Inflammation 2007, 30:105-117. 10.1007/s10753-007-9026-2, 17516158.
32. Kleemann R, Gervois PP, Verschuren L, Staels B, Princen HM, Kooistra T. Fibrates down-regulate IL-1-stimulated C-reactive protein gene expression in hepatocytes by reducing nuclear p50-NFkappa B-C/EBP-beta complex formation. Blood 2003, 101:545-551. 10.1182/blood-2002-06-1762, 12393563.
33. Kleemann R, Verschuren L, De Rooij BJ, Lindeman J, De Maat MM, Szalai AJ, Princen HM, Kooistra T. Evidence for anti-inflammatory activity of statins and PPARalpha activators in human C-reactive protein transgenic mice in vivo and in cultured human hepatocytes in vitro. Blood 2004, 103:4188-4194. 10.1182/blood-2003-11-3791, 14976045.
34. Gervois P, Kleemann R, Pilon A, Percevault F, Koenig W, Staels B, Kooistra T. Global suppression of IL-6-induced acute phase response gene expression after chronic in vivo treatment with the peroxisome proliferator-activated receptor-alpha activator fenofibrate. J Biol Chem 2004, 279:16154-16160. 10.1074/jbc.M400346200, 14764586.
35. Gervois P, Vu-Dac N, Kleemann R, Kockx M, Dubois G, Laine B, Kosykh V, Fruchart JC, Kooistra T, Staels B. Negative regulation of human fibrinogen gene expression by peroxisome proliferator-activated receptor alpha agonists via inhibition of CCAAT box/enhancer-binding protein beta. J Biol Chem 2001, 276:33471-33477. 10.1074/jbc.M102839200, 11418615.
36. Verschuren L, Kleemann R, Offerman EH, Szalai AJ, Emeis SJ, Princen HM, Kooistra T. Effect of low dose atorvastatin versus diet-induced cholesterol lowering on atherosclerotic lesion progression and inflammation in apolipoprotein E*3-Leiden transgenic mice. Arterioscler Thromb Vasc Biol 2005, 25:161-167.
37. Nikolsky Y, Kleemann R. Systems Biology approaches to the study of cardiovascular drugs. Methods Mol Biol 2010, 662:221-243. 10.1007/978-1-60761-800-3_11, 20824474.
38. Wheelock CE, Wheelock AM, Kawashima S, Diez D, Kanehisa M, van Erk M, Kleemann R, Haeggström JZ, Goto S. Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol Biosyst 2009, 5:588-602. 10.1039/b902356a, 19462016.