Transcriptomic coordination in the human metabolic network reveals links between n-3 fat intake, adipose tissue gene expression and metabolic health

PLoS Computational Biology

Volumn 7, Issue 11, 2011, Pages

  Morine, Melissa J ^a   Tierney, Audrey C ^a   van Ommen, Ben ^b   Daniel, Hannelore ^c   Toomey, Sinead ^a   Gjelstad, Ingrid M F ^d,e   Gormley, Isobel C ^a   Pérez Martinez, Pablo ^f   Drevon, Christian A ^d   López Miranda, Jose ^f   Roche, Helen M ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b TNO   (Netherlands)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d UNIVERSITY OF OSLO   (Norway)

^e OSLO UNIVERSITY HOSPITAL   (Norway)

^f HOSPITAL UNIVERSITARIO REINA SOFÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

NUTRITION; TISSUE; TRANSCRIPTION;

ADIPOSE TISSUE; DIETARY RECORDS; GENES EXPRESSION; METABOLIC NETWORK; MOLECULAR LINKS; NETWORK-BASED APPROACH; PATHWAY ANALYSIS; SUBNETWORKS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

METABOLISM;

8 ISOPROSTAGLANDIN F2 ALPHA; OMEGA 3 FATTY ACID; TRANSCRIPTION FACTOR; TRIACYLGLYCEROL;

ADIPOGENESIS; ADIPOSE TISSUE; ADULT; AGED; ARTICLE; CONTROLLED STUDY; DIETARY INTAKE; FAT INTAKE; FEMALE; GENE EXPRESSION; GENETIC ASSOCIATION; HEALTH STATUS; HUMAN; HUMAN TISSUE; LIPID ANALYSIS; LIPID METABOLISM; LIPOGENESIS; MALE; METABOLIC BALANCE; METABOLIC SYNDROME X; METABOLISM; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PROSTAGLANDIN URINE LEVEL; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; BIOLOGICAL MODEL; BIOLOGY; CLINICAL TRIAL; CONTROLLED CLINICAL TRIAL; GENE EXPRESSION PROFILING; GENETICS; MULTICENTER STUDY; MULTIVARIATE ANALYSIS; PROMOTER REGION; RANDOMIZED CONTROLLED TRIAL;

ADIPOGENESIS; ADIPOSE TISSUE; COMPUTATIONAL BIOLOGY; FATTY ACIDS, OMEGA-3; GENE EXPRESSION; GENE EXPRESSION PROFILING; HEALTH STATUS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MULTIVARIATE ANALYSIS; OXIDATIVE STRESS; PROMOTER REGIONS, GENETIC;

EID: 81355164232     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002223     Document Type: Article

References (47)

1. Werner T, (2008) Bioinformatics applications for pathway analysis of microarray data. Curr Op Biotech 19: 50-54.
2. Song S, Black M, (2008) Microarray-based gene set analysis: a comparison of current methods. BMC Bioinf 9: 502.
3. Liu M, Liberzon A, Kong SW, Lai WR, Park PJ, et al. (2007) Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet 3: e96.
4. Zelezniak A, Pers TH, Soares S, Patti ME, Patil KR, (2010) Metabolic Network Topology Reveals Transcriptional Regulatory Signatures of Type 2 Diabetes. PLoS Comput Biol 6: e1000729.
5. del Sol A, Balling R, Hood L, Galas D, (2010) Diseases as network perturbations. Curr Opin Biotech 21: 566-571.
6. Lacroix V, Cottret L, Thébault P, Sagot M-F, (2008) An Introduction to Metabolic Networks and Their Structural Analysis. IEEE/ACM Trans Comput Biol Bioinf 5: 594-617.
7. Wu Z, Zhao X, Chen L, (2009) Identifying responsive functional modules from protein-protein interaction network. Mol Cells 27: 271-277.
8. Buttriss J, Nugent A, (2005) LIPGENE: an integrated approach to tackling the metabolic syndrome. Proc Nutr Soc 64: 345-347.
9. Tierney AC, McMonagle J, Shaw DI, Gulseth HL, Helal O, et al. (2011) Effects of dietary fat modification on insulin sensitivity and on other risk factors of the metabolic syndrome-LIPGENE: a European randomized dietary intervention study. Int J Obes (Lond) 35: 800-809.
10. Shaw DI, Tierney AC, McCarthy S, Uprichard J, Vermunt S, et al. (2008) The Lipgene Food-Exchange Model: a tool to enable investigation of four diets distinct in fatty acid composition. Proc Nutr Soc 67: E86.
11. Kim-Anh LC, Debra R, Christèle R-G, Philippe B, (2008) A Sparse PLS for Variable Selection when Integrating Omics Data. Stat Appl Genet Mol Biol 7: 35.
12. Le Cao K-A, Gonzalez I, Dejean S, (2009) integrOmics: an R package to unravel relationships between two omics datasets. Bioinformatics 25: 2855-2856.
13. Tenenhaus M, (1998) La régression PLS: théorie et pratique. Paris Editions TECHNIP 254 p.
14. Ignacio Gonzalez, (2007) Analyse Canonique Régularisée pour des données fortement multidimensionnelles. PhD Thesis Institut de Mathématiques de Toulouse 134 p.
15. Ma H, Sorokin A, Mazein A, Selkov A, Selkov E, et al. (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 3: 135-135.
16. Ma H-W, Zeng A-P, (2003) The connectivity structure, giant strong component and centrality of metabolic networks. Bioinf 19: 1423-1430.
17. Akaike H, (1974) A new look at the statistical model identification. IEEE Trans Autom Control 19: 716-723.
18. Dijkstra EW, (1959) A note on two problems in connexion with graphs. Numerische Mathematik 1: 269-271.
19. Tonon L, Touzet H, Varre J-S, (2010) TFM-Explorer: mining cis-regulatory regions in genomes. Nucleic Acids Res 38: W286-W292.
20. Dougherty R, Galli C, Ferro-Luzzi A, Iacono J, (1987) Lipid and phospholipid fatty acid composition of plasma, red blood cells, and platelets and how they are affected by dietary lipids: a study of normal subjects from Italy, Finland, and the USA. Am J Clin Nutr 45: 443-455.
21. Reichardt J, Bornholdt S, (2006) Statistical mechanics of community detection. Phys Rev E Stat Nonlin Soft Matter Phys 74: 016110.
22. Theken KN, Deng Y, Kannon MA, Miller TM, Poloyac SM, et al. (2011) Activation of the acute inflammatory response alters cytochrome P450 expression and eicosanoid metabolism. Drug Metab Dispos 39: 22-9.
23. Tsai IJ, Croft KD, Mori TA, Falck JR, Beilin LJ, et al. (2009) 20-HETE and F2-isoprostanes in the metabolic syndrome: the effect of weight reduction. Free Radic Biol Med 46: 263-270.
24. Birsoy K, Chen Z, Friedman J, (2008) Transcriptional Regulation of Adipogenesis by KLF4. Cell Metab 7: 339-347.
25. Fajas L, Landsberg RL, Huss-Garcia Y, Sardet C, Lees JA, et al. (2002) E2Fs regulate adipocyte differentiation. Dev Cell 3: 39-49.
26. Hescott BJ, Leiserson MDM, Cowen LJ, Slonim DK, (2010) Evaluating between-pathway models with expression data. J Comput Biol 17: 477-487.
27. Newton AC, (2009) Lipid activation of protein kinases. J Lipid Res 50 Suppl pp. S266-271.
28. Mérida I, Avila-Flores A, Merino E, (2008) Diacylglycerol kinases: at the hub of cell signalling. Biochem J 409: 1-18.
29. Brindley DN, (2004) Lipid phosphate phosphatases and related proteins: signaling functions in development, cell division, and cancer. J Cell Biochem 92: 900-912.
30. Vedin I, Cederholm T, Freund-Levi Y, Basun H, Hjorth E, et al. (2010) Reduced prostaglandin F2 alpha release from blood mononuclear leukocytes after oral supplementation of omega3 fatty acids: the OmegAD study. J Lipid Res 51: 1179-1185.
31. Mori TA, Puddey IB, Burke V, Croft KD, Dunstan DW, et al. (2000) Effect of omega 3 fatty acids on oxidative stress in humans: GC-MS measurement of urinary F2-isoprostane excretion. Redox Rep 5: 45-46.
32. Mas E, Woodman RJ, Burke V, Puddey IB, Beilin LJ, et al. (2010) The omega-3 fatty acids EPA and DHA decrease plasma F(2)-isoprostanes: Results from two placebo-controlled interventions. Free Radic Res 44: 983-990.
33. Simopoulos AP, (2002) Omega-3 Fatty Acids in Inflammation and Autoimmune Diseases. J Am Coll Nutr 21: 495-505.
34. Oh DY, Talukdar S, Bae EJ, Imamura T, Morinaga H, et al. (2010) GPR120 is an omega-3 fatty acid receptor mediating potent anti-inflammatory and insulin-sensitizing effects. Cell 142: 687-698.
35. Petersson H, Risérus U, McMonagle J, Gulseth HL, Tierney AC, et al. (2010) Effects of Dietary Fat Modification on Oxidative Stress and Inflammatory Markers in the LIPGENE Study. Br J Nutr FirstView pp. 1-6.
36. Kaczynski J, Cook T, Urrutia R, (2003) Sp1- and Krüppel-like transcription factors. Genome Biol 4: 206.
37. Shie JL, Chen ZY, Fu M, Pestell RG, Tseng CC, (2000) Gut-enriched Krüppel-like factor represses cyclin D1 promoter activity through Sp1 motif. Nucleic Acids Res 28: 2969-2976.
38. Marion-Letellier R, Déchelotte P, Iacucci M, Ghosh S, (2009) Dietary modulation of peroxisome proliferator-activated receptor gamma. Gut 58: 586-593.
39. Siersbaek R, Nielsen R, Mandrup S, (2010) PPARgamma in adipocyte differentiation and metabolism--novel insights from genome-wide studies. FEBS Lett 584: 3242-3249.
40. Martin H, (2009) Role of PPAR-gamma in inflammation. Prospects for therapeutic intervention by food components. Mutat Res 669: 1-7.
41. White UA, Stephens JM, (2010) Transcriptional factors that promote formation of white adipose tissue. Mol Cell Endocrinol 318: 10-14.
42. Nunn A, Bell J, Barter P, (2007) The integration of lipid-sensing and anti-inflammatory effects: how the PPARs play a role in metabolic balance. Nucl Recept 5: 1.
43. Chambrier C, Bastard JP, Rieusset J, Chevillotte E, Bonnefont-Rousselot D, et al. (2002) Eicosapentaenoic acid induces mRNA expression of peroxisome proliferator-activated receptor gamma. Obes Res 10: 518-525.
44. Hanada H, Morikawa K, Hirota K, Nonaka M, Umehara Y, (2010) Induction of apoptosis and lipogenesis in human preadipocyte cell line by N-3 PUFAs. Cell Biol Int 35: 51-59.
45. Colomer R, Moreno-Nogueira JM, García-Luna PP, García-Peris P, García-de-Lorenzo A, et al. (2007) N-3 fatty acids, cancer and cachexia: a systematic review of the literature. Br J Nutr 97: 823-831.
46. Irving GF, Freund-Levi Y, Eriksdotter-Jönhagen M, Basun H, Brismar K, et al. (2009) Omega-3 fatty acid supplementation effects on weight and appetite in patients with Alzheimer's disease: the omega-3 Alzheimer's disease study. J Am Geriatr Soc 57: 11-17.
47. Perez-Martinez P, Perez-Jimenez F, Lopez-Miranda J, (2010) n-3 PUFA and lipotoxicity. BBA-Mol Cell L 1801: 362-366.