Angiogenesis

, Volume 12, Issue 3, pp 221–229 | Cite as

Analysis of PPARα-dependent and PPARα-independent transcript regulation following fenofibrate treatment of human endothelial cells

  • Hiromitsu Araki
  • Yoshinori Tamada
  • Seiya Imoto
  • Ben Dunmore
  • Deborah Sanders
  • Sally Humphrey
  • Masao Nagasaki
  • Atsushi Doi
  • Yukiko Nakanishi
  • Kaori Yasuda
  • Yuki Tomiyasu
  • Kousuke Tashiro
  • Cristin Print
  • D. Stephen Charnock-Jones
  • Satoru Kuhara
  • Satoru Miyano
Original Paper

Abstract

Fenofibrate is a synthetic ligand for the nuclear receptor peroxisome proliferator-activated receptor (PPAR) alpha and has been widely used in the treatment of metabolic disorders, especially hyperlipemia, due to its lipid-lowering effect. The molecular mechanism of lipid-lowering is relatively well defined: an activated PPARα forms a PPAR–RXR heterodimer and this regulates the transcription of genes involved in energy metabolism by binding to PPAR response elements in their promoter regions, so-called “trans-activation”. In addition, fenofibrate also has anti-inflammatory and anti-athrogenic effects in vascular endothelial and smooth muscle cells. We have limited information about the anti-inflammatory mechanism of fenofibrate; however, “trans-repression” which suppresses production of inflammatory cytokines and adhesion molecules probably contributes to this mechanism. Furthermore, there are reports that fenofibrate affects endothelial cells in a PPARα-independent manner. In order to identify PPARα-dependently and PPARα-independently regulated transcripts, we generated microarray data from human endothelial cells treated with fenofibrate, and with and without siRNA-mediated knock-down of PPARα. We also constructed dynamic Bayesian transcriptome networks to reveal PPARα-dependent and -independent pathways. Our transcriptome network analysis identified growth differentiation factor 15 (GDF15) as a hub gene having PPARα-independently regulated transcripts as its direct downstream children. This result suggests that GDF15 may be PPARα-independent master-regulator of fenofibrate action in human endothelial cells.

Keywords

Endothelial cells Fenofibrate PPARα Transcriptome network 

Notes

Acknowledgments

The authors would like to thank two reviewers for their constructive comments and suggestions. Computation time was provided by the Super Computer System, Human Genome Center, Institute of Medical Science, University of Tokyo.

Supplementary material

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References

  1. 1.
    Lefebvre P, Chinetti G, Fruchart JC, Staels B (2006) Sorting out the roles of PPARα in energy metabolism and vascular homeostasis. J Clin Invest 116:571–580. doi:10.1172/JCI27989 PubMedCrossRefGoogle Scholar
  2. 2.
    Gervois P, Fruchart JC, Staels B (2007) Drug insight: mechanisms of action and therapeutic applications for agonists of peroxisome proliferator-activated receptors. Nat Clin Pract Endocrinol Metab 3:145–156. doi:10.1038/ncpendmet0397 PubMedCrossRefGoogle Scholar
  3. 3.
    Staels B, Maes M, Zambon A (2008) Fibrates and future PPARα agonists in the treatment of cardiovascular disease. Nat Clin Pract Cardiovasc Med 5:542–553. doi:10.1038/ncpcardio1278 PubMedCrossRefGoogle Scholar
  4. 4.
    Zandbergen F, Plutzky J (2007) PPARα in atherosclerosis and inflammation. Biochim Biophys Acta 1771:972–982PubMedGoogle Scholar
  5. 5.
    Kim J, Ahn JH, Kim JH, Yu YS, Kim HS, Ha J, Shinn SH, Oh YS (2007) Fenofibrate regulates retinal endothelial cell survival through the AMPK signal transduction pathway. Exp Eye Res 84:886–893. doi:10.1016/j.exer.2007.01.009 PubMedCrossRefGoogle Scholar
  6. 6.
    Murakami H, Murakami R, Kambe F, Cao X, Takahashi R, Asai T, Hirai T, Numaguchi Y, Okumura K, Seo H, Murohara T (2006) Fenofibrate activates AMPK and increases eNOS phosphorylation in HUVEC. Biochem Biophys Res Commun 341:973–978. doi:10.1016/j.bbrc.2006.01.052 PubMedCrossRefGoogle Scholar
  7. 7.
    Affara M, Dunmore B, Savoie C, Imoto S, Tamada Y, Araki H, Charnock-Jones DS, Miyano S, Print C (2007) Understanding endothelial cell apoptosis: what can the transcriptome, glycome and proteome reveal? Philos Trans R Soc Lond B Biol Sci 362:1469–1487. doi:10.1098/rstb.2007.2129 PubMedCrossRefGoogle Scholar
  8. 8.
    Spagnou S, Miller AD, Keller M (2004) Lipidic carriers of siRNA: differences in the formulation, cellular uptake, and delivery with plasmid DNA. Biochemistry 43:13348–13356. doi:10.1021/bi048950a PubMedCrossRefGoogle Scholar
  9. 9.
    Tamada Y, Araki H, Imoto S, Nagasaki M, Doi A, Nakanishi Y, Tomiyasu Y, Yasuda K, Dunmore B, Sanders D, Humphries S, Print C, Charnock-Jones DS, Sanders D, Tashiro K, Kuhara S, Miyano S (2009) Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks. Pac Symp Biocomput 14:251–263Google Scholar
  10. 10.
    Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–5121. doi:10.1073/pnas.091062498 PubMedCrossRefGoogle Scholar
  11. 11.
    Gupta PK, Yoshida R, Imoto S, Yamaguchi R, Miyano S (2007) Statistical absolute evaluation of gene ontology terms with gene expression data. Proceedings of the 3rd international symposium on bioinformatics research and applications. Lecture note in Bioinformatics, vol 4463. Springer-Verlag, pp 146–157Google Scholar
  12. 12.
    Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57:289–300Google Scholar
  13. 13.
    Kim S, Imoto S, Miyano S (2004) Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data. Biosystems 75:57–65. doi:10.1016/j.biosystems.2004.03.004 PubMedCrossRefGoogle Scholar
  14. 14.
    Gervois P, Vu-Dac N, Kleemann R, Kockx M, Dubois G, Laine B, Kosykh V, Fruchart JC, Kooistra T, Staels B (2001) 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 276:33471–33477. doi:10.1074/jbc.M102839200 PubMedCrossRefGoogle Scholar
  15. 15.
    Goya K, Sumitani S, Xu X, Kitamura T, Yamamoto H, Kurebayashi S, Saito H, Kouhara H, Kasayama S, Kawase I (2004) Peroxisome proliferator-activated receptor α agonists increase nitric oxide synthase expression in vascular endothelial cells. Arterioscler Thromb Vasc Biol 24:658–663. doi:10.1161/01.ATV.0000118682.58708.78 PubMedCrossRefGoogle Scholar
  16. 16.
    Panigrahy D, Kaipainen A, Huang S, Butterfield CE, Barnés CM, Fannon M, Laforme AM, Chaponis DM, Folkman J, Kieran MW (2008) PPARα agonist fenofibrate suppresses tumor growth through direct and indirect angiogenesis inhibition. Proc Natl Acad Sci USA 105:985–990. doi:10.1073/pnas.0711281105 PubMedCrossRefGoogle Scholar
  17. 17.
    Sands WA, Martin AF, Strong EW, Palmer TM (2004) Specific inhibition of nuclear factor-kappaB-dependent inflammatory responses by cell type-specific mechanisms upon A2A adenosine receptor gene transfer. Mol Pharmacol 66:1147–1159. doi:10.1124/mol.104.001107 PubMedCrossRefGoogle Scholar
  18. 18.
    Goetze S, Eilers F, Bungenstock A, Kintscher U, Stawowy P, Blaschke F, Graf K, Law RE, Fleck E, Gräfe M (2002) PPAR activators inhibit endothelial cell migration by targeting Akt. Biochem Biophys Res Commun 293:1431–1437. doi:10.1016/S0006-291X(02)00385-6 PubMedCrossRefGoogle Scholar
  19. 19.
    Cooper TF, Morby AP, Gunn A, Schneider D (2006) Effect of random and hub gene disruptions on environmental and mutational robustness in Escherichia coli. BMC Genomics 7:237. doi:10.1186/1471-2164-7-237 PubMedCrossRefGoogle Scholar
  20. 20.
    Zotenko E, Mestre J, O’Leary DP, Przytycka TM (2008) Why do hubs in the yeast protein interaction network tend to be essential: reexamining the connection between the network topology and essentiality. PLOS Comput Biol 4:e1000140. doi:10.1371/journal.pcbi.1000140 PubMedCrossRefGoogle Scholar
  21. 21.
    Abdollahi A, Schwager C, Kleeff J, Esposito I, Domhan S, Peschke P, Hauser K, Hahnfeldt P, Hlatky L, Debus J, Peters JM, Friess H, Folkman J, Huber PE (2007) Transcriptional network governing the angiogenic switch in human pancreatic cancer. Proc Natl Acad Sci USA 104:12890–12895. doi:10.1073/pnas.0705505104 PubMedCrossRefGoogle Scholar
  22. 22.
    Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37:382–390. doi:10.1038/ng1532 PubMedCrossRefGoogle Scholar
  23. 23.
    Yamamoto T, Nishizaki I, Nukada T, Kamegaya E, Furuya S, Hirabayashi Y, Ikeda K, Hata H, Kobayashi H, Sora I, Yamamoto H (2004) Functional identification of ASCT1 neutral amino acid transporter as the predominant system for the uptake of l-serine in rat neurons in primary culture. Neurosci Res 49:101–111. doi:10.1016/j.neures.2004.02.004 PubMedCrossRefGoogle Scholar
  24. 24.
    Ago T, Sadoshima J (2006) GDF15, a cardioprotective TGF-beta superfamily protein. Circ Res 98:294–297. doi:10.1161/01.RES.0000207919.83894.9d PubMedCrossRefGoogle Scholar
  25. 25.
    Ferrari N, Pfeffer U, Dell’Eva R, Ambrosini C, Noonan DM, Albini A (2005) The transforming growth factor-beta family members bone morphogenetic protein-2 and macrophage inhibitory cytokine-1 as mediators of the antiangiogenic activity of N-(4-hydroxyphenyl) retinamide. Clin Cancer Res 11:4610–4619. doi:10.1158/1078-0432.CCR-04-2210 PubMedCrossRefGoogle Scholar
  26. 26.
    Huang CY, Beer TM, Higano CS, True LD, Vessella R, Lange PH, Garzotto M, Nelson PS (2007) Molecular alterations in prostate carcinomas that associate with in vivo exposure to chemotherapy: identification of a cytoprotective mechanism involving growth differentiation factor 15. Clin Cancer Res 13:5825–5833. doi:10.1158/1078-0432.CCR-07-1037 PubMedCrossRefGoogle Scholar
  27. 27.
    Lin R, Liu J, Gan W, Yang G (2004) C-reactive protein-induced expression of CD40-CD40L and the effect of lovastatin and fenofibrate on it in human vascular endothelial cells. Biol Pharm Bull 27:1537–1543. doi:10.1248/bpb.27.1537 PubMedCrossRefGoogle Scholar
  28. 28.
    Martinez JM, Sali T, Okazaki R, Anna C, Hollingshead M, Hose C, Monks A, Walker NJ, Baek SJ, Eling TE (2006) Drug-induced expression of nonsteroidal anti-inflammatory drug-activated gene/macrophage inhibitory cytokine-1/prostate-derived factor, a putative tumor suppressor, inhibits tumor growth. J Pharmacol Exp Ther 318:899–906. doi:10.1124/jpet.105.100081 PubMedCrossRefGoogle Scholar
  29. 29.
    Holland CM, Saidi SA, Evans AL, Sharkey AM, Latimer JA, Crawford RA, Charnock-Jones DS, Print C, Smith SK (2004) Transcriptome analysis of endometrial cancer identifies peroxisome proliferator-activated receptors as potential therapeutic targets. Mol Cancer Ther 3:993–1001PubMedGoogle Scholar
  30. 30.
    Baek SJ, Kim JS, Nixon JB, DiAugustine RP, Eling TE (2004) Expression of NAG-1, a transforming growth factor-beta superfamily member, by troglitazone requires the early growth response gene EGR-1. J Biol Chem 279:6883–6892. doi:10.1074/jbc.M305295200 PubMedCrossRefGoogle Scholar
  31. 31.
    Chintharlapalli S, Papineni S, Baek SJ, Liu S, Safe S (2005) 1,1-Bis(3′-indolyl)-1-(p-substitutedphenyl)methanes are peroxisome proliferator-activated receptor gamma agonists but decrease HCT-116 colon cancer cell survival through receptor-independent activation of early growth response-1 and nonsteroidal anti-inflammatory drug-activated gene-1. Mol Pharmacol 68:1782–1792PubMedGoogle Scholar
  32. 32.
    Yamaguchi K, Lee SH, Eling TE, Baek SJ (2006) A novel peroxisome proliferator-activated receptor gamma ligand, MCC-555, induces apoptosis via posttranscriptional regulation of NAG-1 in colorectal cancer cells. Mol Cancer Ther 5:1352–1361. doi:10.1158/1535-7163.MCT-05-0528 PubMedCrossRefGoogle Scholar
  33. 33.
    Baek SJ, Wilson LC, Hsi LC, Eling TE (2003) Troglitazone, a peroxisome proliferator-activated receptor gamma (PPAR gamma) ligand, selectively induces the early growth response-1 gene independently of PPAR gamma. A novel mechanism for its anti-tumorigenic activity. J Biol Chem 278:5845–5853. doi:10.1074/jbc.M208394200 PubMedCrossRefGoogle Scholar
  34. 34.
    Duhaney TA, Cui L, Rude MK, Lebrasseur NK, Ngoy S, De Silva DS, Siwik DA, Liao R, Sam F (2007) Peroxisome proliferator-activated receptor alpha-independent actions of fenofibrate exacerbates left ventricular dilation and fibrosis in chronic pressure overload. Hypertension 49:1084–1094. doi:10.1161/HYPERTENSIONAHA.107.086926 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Hiromitsu Araki
    • 1
    • 7
  • Yoshinori Tamada
    • 2
  • Seiya Imoto
    • 2
  • Ben Dunmore
    • 3
  • Deborah Sanders
    • 3
  • Sally Humphrey
    • 3
  • Masao Nagasaki
    • 2
  • Atsushi Doi
    • 1
    • 7
  • Yukiko Nakanishi
    • 1
    • 7
  • Kaori Yasuda
    • 1
    • 7
  • Yuki Tomiyasu
    • 1
    • 7
  • Kousuke Tashiro
    • 5
  • Cristin Print
    • 6
  • D. Stephen Charnock-Jones
    • 3
    • 4
  • Satoru Kuhara
    • 5
  • Satoru Miyano
    • 2
  1. 1.Systems Pharmacology Research InstituteGNI LtdFukuokaJapan
  2. 2.Human Genome Center, Institute of Medical ScienceThe University of TokyoTokyoJapan
  3. 3.Department of Obstetrics and GynaecologyUniversity of CambridgeCambridgeUK
  4. 4.Cambridge National Institute for Health Research Biomedical Research CentreCambridgeUK
  5. 5.Graduate School of Genetic Resources TechnologyKyushu UniversityFukuokaJapan
  6. 6.Department of Molecular Medicine and Pathology, School of Medical SciencesThe University of AucklandAucklandNew Zealand
  7. 7.Cell Innovator Inc.FukuokaJapan

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