A map of the PPARα transcription regulatory network for primary human hepatocytes

Chemico-Biological Interactions

Volumn 209, Issue 1, 2014, Pages 14-24

  McMullen, Patrick D ^a   Bhattacharya, Sudin ^a   Woods, Courtney G ^a   Sun, Bin ^a   Yarborough, Kathy ^a   Ross, Susan M ^a   Miller, Manda E ^a   McBride, Mary T ^b   Lecluyse, Edward L ^a   Clewell, Rebecca A ^a   Andersen, Melvin E ^a  

^a HAMNER INSTITUTES FOR HEALTH SCIENCES   (United States)

^b Government Relations Life Sciences and Chemical Analysis   (United States)

Author keywords

High throughput technologies; Toxicity pathways; TT21C

Indexed keywords

2 [4 [2 [3 CYCLOHEXYL 1 (4 CYCLOHEXYLBUTYL)UREIDO]ETHYL]PHENYLTHIO] 2 METHYLPROPIONIC ACID; ESTROGEN RECEPTOR ALPHA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR ALPHA; PROTEIN KINASE; STAT1 PROTEIN; TRANSCRIPTION FACTOR ETS 1; TRANSCRIPTION FACTOR SP1;

ARTICLE; BINDING SITE; CONTROLLED STUDY; FATTY ACID METABOLISM; GENE EXPRESSION; GENE REGULATORY NETWORK; HUMAN; HUMAN CELL; LIPID METABOLISM; LIPID TRANSPORT; LIVER CELL; PEROXISOME PROLIFERATOR RESPONSE ELEMENT; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS;

HIGH-THROUGHPUT TECHNOLOGIES; TOXICITY PATHWAYS; TT21C;

BINDING SITES; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DOSE-RESPONSE RELATIONSHIP, DRUG; DOWN-REGULATION; HEPATOCYTES; HUMANS; MICROARRAY ANALYSIS; PPAR ALPHA; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC; UP-REGULATION;

EID: 84891514922     PISSN: 00092797     EISSN: 18727786     Source Type: Journal    
DOI: 10.1016/j.cbi.2013.11.006     Document Type: Article

References (71)

1. M.E. Andersen, and D. Krewski Toxicity testing in the 21st century: bringing the vision to life Toxicol. Sci. 107 2 2009 324 330
2. M.E. Andersen, and D. Krewski The vision of toxicity testing in the 21st century: moving from discussion to action Toxicol. Sci. 117 1 2010 17 24
3. NRC, Toxicity Testing in the 21st Century: A Vision and a Strategy, The National Academies Press, Washington, DC, 2007.
4. M.V. Chakravarthy et al. Identification of a physiologically relevant endogenous ligand for PPARalpha in liver Cell 138 3 2009 476 488
5. P. Lefebvre et al. Sorting out the roles of PPARα in energy metabolism and vascular homeostasis J. Clin. Invest. 116 3 2006 571 580 (Pubitemid 43326861)
6. S. Mandard, M. Müller, and S. Kersten Peroxisome proliferator-activated receptor α target genes Cell. Mol. Life Sci. 61 4 2004 393 416 (Pubitemid 38316578)
7. L. Michalik, and W. Wahli PPARs mediate lipid signaling in inflammation and cancer PPAR Res. 2008 Article ID 134059
8. F. Zandbergen, and J. Plutzky PPARα in atherosclerosis and inflammation Biochim. Biophys. Acta. Mol. Cell Biol. Lipids 1771 8 2007 972 982
9. S.J. Bensinger, and P. Tontonoz Integration of metabolism and inflammation by lipid-activated nuclear receptors Nature 454 7203 2008 470 477
10. J.K. Reddy, D.L. Azarnoff, and C.E. Hignite Hypolipidaemic hepatic peroxisome proliferators form a novel class of chemical carcinogens Nature 283 5745 1980 397 398 (Pubitemid 10125816)
11. J.K. Reddy, M.S. Rao, and D.E. Moody Hepatocellular carcinomas in acatalasemic mice treated with Nafenopin, a hypolipidemic peroxisome proliferator Cancer Res. 36 4 1976 1211 1217
12. J.D. Tugwood et al. The mouse peroxisome proliferator activated receptor recognizes a response element in the 5′ flanking sequence of the rat acyl CoA oxidase gene EMBO J. 11 2 1992 433 439
13. C. Dreyer et al. Control of the peroxisomal beta-oxidation pathway by a novel family of nuclear hormone receptors Cell 68 5 1992 879 887
14. D.L. van der Meer et al. Profiling of promoter occupancy by PPARalpha in human hepatoma cells via ChIP-chip analysis Nucleic Acids Res. 38 9 2010 2839 2850
15. M.B. Rosen et al. Gene profiling in the livers of wild-type and PPARalpha-null mice exposed to perfluorooctanoic acid Toxicol. Pathol. 36 4 2008 592 607
16. R.K. Semple et al. A dominant negative human peroxisome proliferator-activated receptor (PPAR){alpha} is a constitutive transcriptional corepressor and inhibits signaling through all PPAR isoforms Endocrinology 146 4 2005 1871 1882 (Pubitemid 40396897)
17. P.J. Brown et al. Identification of a subtype selective human PPARalpha agonist through parallel-array synthesis Bioorg. Med. Chem. Lett. 11 9 2001 1225 1227 (Pubitemid 32406090)
18. R.A. Irizarry et al. Summaries of affymetrix GeneChip probe level data Nucleic Acids Res. 31 4 2003 e15
19. Y. Benjamini, and Y. Hochberg Controlling the false discovery rate - a practical and powerful approach to multiple testing J. Royal Stat. Soc. B Method. 57 1 1995 289 300
20. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 14 2009 1754 1760
21. Y. Zhang et al. Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 9 2008 R137
22. P. Machanick, and T.L. Bailey MEME-ChIP: motif analysis of large DNA datasets Bioinformatics 27 12 2011 1696 1697
23. T.L. Bailey et al. MEME SUITE: tools for motif discovery and searching Nucleic Acids Res. 37 Web Server issue 2009 W202 8
24. U. Varanasi et al. Identification of a peroxisome proliferator-responsive element upstream of the human peroxisomal fatty acyl coenzyme A oxidase gene J. Biol. Chem. 271 4 1996 2147 2155 (Pubitemid 26047804)
25. C. Mascaro et al. Control of human muscle-type carnitine palmitoyltransferase I gene transcription by peroxisome proliferator-activated receptor J. Biol. Chem. 273 15 1998 8560 8563 (Pubitemid 28176129)
26. L. Napal, P.F. Marrero, and D. Haro An intronic peroxisome proliferator-activated receptor-binding sequence mediates fatty acid induction of the human carnitine palmitoyltransferase 1A J. Mol. Biol. 354 4 2005 751 759 (Pubitemid 41735500)
27. M. Nagasawa et al. Identification of a functional peroxisome proliferator-activated receptor (PPAR) response element (PPRE) in the human apolipoprotein A-IV gene Biochem. Pharmacol. 78 5 2009 523 530
28. M. Rakhshandehroo et al. Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human PLoS ONE 4 8 2009 e6796
29. J.S. Carroll et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1 Cell 122 1 2005 33 43 (Pubitemid 40977938)
30. J.S. Carroll et al. Genome-wide analysis of estrogen receptor binding sites Nat. Genet. 38 11 2006 1289 1297 (Pubitemid 44646291)
31. C.L. George, S.L. Lightman, and S.C. Biddie Transcription factor interactions in genomic nuclear receptor function Epigenomics 3 4 2011 471 485
32. N. Viswakarma et al. Coactivators in PPAR-Regulated Gene Expression PPAR Res. 2010 2010
33. N. Vu-Dac et al. Fibrates increase human apolipoprotein A-II expression through activation of the peroxisome proliferator-activated receptor J. Clin. Invest. 96 2 1995 741 750
34. P. Targett-Adams et al. A PPAR response element regulates transcription of the gene for human adipose differentiation-related protein Biochim. Biophys. Acta 1728 1-2 2005 95 104 (Pubitemid 40409959)
35. E. Seree et al. Evidence for a new human CYP1A1 regulation pathway involving PPAR-alpha and 2 PPRE sites Gastroenterology 127 5 2004 1436 1445 (Pubitemid 39457770)
36. V. Matys et al. TRANSFAC: transcriptional regulation, from patterns to profiles Nucleic Acids Res. 31 1 2003 374 378 (Pubitemid 36150406)
37. W. Huang da, B.T. Sherman, and R.A. Lempicki Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists Nucleic Acids Res. 37 1 2009 1 13
38. M. Rakhshandehroo et al. Comprehensive analysis of PPARalpha-dependent regulation of hepatic lipid metabolism by expression profiling PPAR Res. 2007 2007 26839
39. J.D. Stender et al. Genome-wide analysis of estrogen receptor α DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation Mol. Cell. Biol. 30 16 2010 3943 3955
40. T.E. Reddy et al. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation Genome Res. 19 12 2009 2163 2171
41. A.Y. So et al. Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor PLoS Genetics 3 6 2007
42. N. Heldring et al. Estrogen receptors: how do they signal and what are their targets Physiol. Rev. 87 3 2007 905 931 (Pubitemid 47084672)
43. V. Bourdeau et al. Genome-wide identification of high-affinity estrogen response elements in human and mouse Mol. Endocrinol. 18 6 2004 1411 1427 (Pubitemid 38692179)
44. C. Tudor et al. Association with coregulators is the major determinant governing peroxisome proliferator-activated receptor mobility in living cells J. Biol. Chem. 282 7 2007 4417 4426 (Pubitemid 47100921)
45. O.S. Gardner et al. Dependence of peroxisome proliferator-activated receptor ligand-induced mitogen-activated protein kinase signaling on epidermal growth factor receptor transactivation J. Biol. Chem. 278 47 2003 46261 46269 (Pubitemid 37452196)
46. T. Teruel et al. Rosiglitazone and retinoic acid induce uncoupling protein-1 (UCP-1) in a p38 mitogen-activated protein kinase-dependent manner in fetal primary brown adipocytes J. Biol. Chem. 278 1 2003 263 269 (Pubitemid 36043571)
47. B.J. Ledwith et al. Growth regulation by peroxisome proliferators: opposing activities in early and late G1 Cancer Res. 56 14 1996 3257 3264 (Pubitemid 26242973)
48. C.L. Rokos, and B.J. Ledwith Peroxisome proliferators activate extracellular signal-regulated kinases in immortalized mouse liver cells J. Biol. Chem. 272 20 1997 13452 13457 (Pubitemid 27216781)
49. C.J. Pauley, B.J. Ledwith, and C. Kaplanski Peroxisome proliferators activate growth regulatory pathways largely via peroxisome proliferator- activated receptor alpha-independent mechanisms Cell. Signal. 14 4 2002 351 358 (Pubitemid 34164690)
50. B.J. Mounho, and B.D. Thrall The extracellular signal-regulated kinase pathway contributes to mitogenic and antiapoptotic effects of peroxisome proliferators in vitro Toxicol. Appl. Pharmacol. 159 2 1999 125 133 (Pubitemid 29426584)
51. A.B. Ropero et al. Rapid non-genomic regulation of Ca2+ signals and insulin secretion by PPAR alpha ligands in mouse pancreatic islets of Langerhans J. Endocrinol. 200 2 2009 127 138
52. S.G. Smith et al. The effect of PPAR agonists on the migration of mature and immature eosinophils PPAR Res. 2012 2012 235231
53. R.C. Cattley Peroxisome proliferators and receptor-mediated hepatic carcinogenesis Toxicol. Pathol. 32 Suppl 2 2004 6 11 (Pubitemid 38993909)
54. J.E. Klaunig et al. PPARalpha agonist-induced rodent tumors: modes of action and human relevance Crit. Rev. Toxicol. 33 6 2003 655 780 (Pubitemid 38037444)
55. F.J. Gonzalez, and Y.M. Shah PPARalpha: mechanism of species differences and hepatocarcinogenesis of peroxisome proliferators Toxicology 246 1 2008 2 8
56. Y. Xu et al. Receptor-type protein-tyrosine phosphatase-kappa regulates epidermal growth factor receptor function J. Biol. Chem. 280 52 2005 42694 42700 (Pubitemid 43049228)
57. S.H. Han et al. VDUP1 upregulated by TGF-beta1 and 1,25-dihydorxyvitamin D3 inhibits tumor cell growth by blocking cell-cycle progression Oncogene 22 26 2003 4035 4046 (Pubitemid 36819644)
58. R.G. Bars et al. Induction of cytochrome P-450 in cultured rat hepatocytes. The heterogeneous localization of specific isoenzymes using immunocytochemistry Biochem. J. 262 1 1989 151 158 (Pubitemid 19220943)
59. R. Sarangapani et al. Dose-response modeling of cytochrome p450 induction in rats by octamethylcyclotetrasiloxane Toxicol. Sci. 67 2 2002 159 172 (Pubitemid 34746469)
60. J.D. Oliver, and R.A. Roberts Receptor-mediated hepatocarcinogenesis: role of hepatocyte proliferation and apoptosis Pharmacol. Toxicol. 91 1 2002 1 7 (Pubitemid 34753746)
61. Q. Zhang, S. Bhattacharya, and M.E. Andersen Ultrasensitive response motifs: basic amplifiers in molecular signalling networks Open Biol. 3 4 2013 130031
62. A. Piskunov and C. Rochette-Egly, MSK1 and Nuclear receptors signaling, in: MSKs, J.S.C. Arthur (Ed.), Landes Biosci, 2013.
63. F. Zassadowski et al. Regulation of the transcriptional activity of nuclear receptors by the MEK/ERK1/2 pathway Cell. Signal. 24 12 2012 2369 2377
64. L. Kang et al. Involvement of estrogen receptor variant ER-alpha36, not GPR30, in nongenomic estrogen signaling Mol. Endocrinol. 24 4 2010 709 721
65. A.W. Norman, M.T. Mizwicki, and D.P. Norman Steroid-hormone rapid actions, membrane receptors and a conformational ensemble model Nat. Rev. Drug Discov. 3 1 2004 27 41 (Pubitemid 38088696)
66. X. Yang et al. Novel membrane-associated androgen receptor splice variant potentiates proliferative and survival responses in prostate cancer cells J. Biol. Chem. 286 41 2011 36152 36160
67. S. Mandard et al. The direct peroxisome proliferator-activated receptor target fasting-induced adipose factor (FIAF/PGAR/ANGPTL4) is present in blood plasma as a truncated protein that is increased by fenofibrate treatment J. Biol. Chem. 279 33 2004 34411 34420 (Pubitemid 39318067)
68. G.S. Yu, Y.C. Lu, and T. Gulick Co-regulation of tissue-specific alternative human carnitine palmitoyltransferase Ibeta gene promoters by fatty acid enzyme substrate J. Biol. Chem. 273 49 1998 32901 32909 (Pubitemid 28557682)
69. H. Poirier et al. Differential involvement of peroxisome-proliferator- activated receptors alpha and delta in fibrate and fatty-acid-mediated inductions of the gene encoding liver fatty-acid-binding protein in the liver and the small intestine Biochem. J. 355 Pt. 2 2001 481 488 (Pubitemid 32397809)
70. M.H. Hsu et al. Identification of peroxisome proliferator-responsive human genes by elevated expression of the peroxisome proliferator-activated receptor alpha in HepG2 cells J. Biol. Chem. 276 30 2001 27950 27958
71. K. Tachibana et al. Regulation of the human SLC25A20 expression by peroxisome proliferator-activated receptor alpha in human hepatoblastoma cells Biochem. Biophys. Res. Commun. 389 3 2009 501 505