High throughput 'omics' approaches to assess the effects of phytochemicals in human health studies

British Journal of Nutrition

Volumn 99, Issue E-SUPPL. 1, 2008, Pages

  Ovesná, Jaroslava ^a   Slabý, Ondřej ^b   Toussaint, Olivier ^c   Kodíček, Milan ^d   Maršík, Petr ^e   Pouchová, Vladimíra ^a   Vaněk, Tomáš ^e  

^a CROP RESEARCH INSTITUTE   (Czech Republic)

^b MASARYK MEMORIAL CANCER INSTITUTE   (Czech Republic)

^c UNIVERSITY OF NAMUR   (Belgium)

^d INSTITUTE OF CHEMICAL TECHNOLOGY   (Czech Republic)

^e INSTITUTE OF EXPERIMENTAL BOTANY   (Czech Republic)

Author keywords

Omics; High throughput platforms; Human health; Nutrigenomics; Phytochemicals

Indexed keywords

DOUBLE STRANDED RNA; FOLIC ACID; GINKGO BILOBA EXTRACT; ISOFLAVONE DERIVATIVE; MICRORNA; PLANT MEDICINAL PRODUCT; PROTEOME; SMALL INTERFERING RNA;

ALLELE; ANTIINFLAMMATORY ACTIVITY; APOPTOSIS; AUTOIMMUNE DISEASE; CANCER RISK; CHRONIC DISEASE; DIET SUPPLEMENTATION; DNA DETERMINATION; DNA METHYLATION; DNA MICROARRAY; DRUG DETERMINATION; DRUG EFFECT; DRUG EFFICACY; DRUG MECHANISM; DRUG METABOLISM; EPIGENETICS; FACTORIAL ANALYSIS; FOOD ANALYSIS; FOOD COMPOSITION; FRUIT; GENE EXPRESSION REGULATION; GENE INTERACTION; GENETIC SCREENING; GENETIC SUSCEPTIBILITY; GENOMICS; GENOTYPE; HAPLOTYPE; HIGH THROUGHPUT SCREENING; HUMAN; LIGHT SCATTERING; MALIGNANT NEOPLASTIC DISEASE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METABOLOMICS; MICROARRAY ANALYSIS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUTRIGENOMICS; NUTRITIONAL HEALTH; NUTRITIONAL VALUE; PROTEIN DETERMINATION; PROTEIN PROCESSING; PROTEOMICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; REVIEW; RISK ASSESSMENT; RISK REDUCTION; RNA ANALYSIS; RNA INTERFERENCE; SERIAL ANALYSIS OF GENE EXPRESSION; SINGLE NUCLEOTIDE POLYMORPHISM; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; VEGETABLE;

BIOLOGICAL FACTORS; DIET; FOOD; GENE EXPRESSION REGULATION; HUMANS; METABOLOMICS; NUTRIGENOMICS; NUTRITIONAL PHYSIOLOGICAL PHENOMENA; PROTEOMICS;

EID: 52949093172     PISSN: 00071145     EISSN: 14752662     Source Type: Journal    
DOI: 10.1017/S0007114508965818     Document Type: Review

References (65)

1. Kaput J & Rodriguez RL (2004) Nutritional genomics: The next frontier for post genomic era. Physiol Genomics 16, 166-177.
2. Vaarala O (2006) Is it dietary insulin? Ann N Y Acad Sci 1079 350-359.
3. Kaput J & Rodriguez RL (2004) Nutritional genomics: The next frontier for post genomic era. Physiol Genomics 16, 166-177.
4. Ames BN (2005) Increasing longevity by tuning-up metabolism. EMBO Rep 6, S1, S20-S24.
5. Prentier R (2002) Phytochemical composition: Paradigm shift for food-health considerations. Asia Pac J Clin Nutr 11, S197-S201.
6. Rotelli AE, Guardia T, Juarez AO, de la Rocha NE & Pelzer LE (2003) Comparative study of flavonoids in experimental models of inflammation. Pharmacol Res 48, 601-606.
7. Williamson G & Manach C (2005) Bioavailability and bioefficacy studies of polyphenols in humans. II. Review of 93 intervention studies. Am J Clin Nutr 81, 243S-255S.
8. Liu RH (2003) Health benefits of fruit and vegetables are from additive and synergistic combinations of phytochemicals. Am J Clin Nutr 78, Suppl., 517S-520S.
9. Heber D (2004) Vegetables, fruits and phytoestrogens in the prevention of diseases. J Postgrad Med 50, 145-149.
10. Galitski T (2004) Molecular Networks In Model systems. Annu Rev Genomics Hum Genet 5, 177-187.
11. Stein LD (2004) Human genome: End of the beginning. Nature 431 915-916.
12. Kaput J (2006) Diet-disease interactions at the molecular level. An experimental paradigm. In Phytochemicals: Nutrient-Gene Interactions pp. 23-39 [M Meskin, WR Bidlack and RK Randoph, editors]. Boca Raton: CRC Press.
13. Serre D & Hudson TJ (2006) Resources for genetic variation studies. Annu Rev Genomics Hum Genet 7, 443-457.
14. The International HapMap Consortiu (2005) A haplotype map of the human genome. Nature 437, 1299-1320.
15. Hesketh J, Wybranska I, Dominels Y, King M, Elliott R, Pico C & Keijer J (2006) Nutrient-gene interactions in benefit-risk analysis. Br J Nutr 95, 1232-1236.
16. Molloy AM & Scott JM (2001) Folates and prevention of disease. Public Health Nutr 4, 601-609.
17. Higdon JV, Delage B, Williams ED & Dashwood RH (2007) Cruciferous vegetables and human cancer risk: Epidemiologic evidence and mechanistic basis. Pharmacol Res 55, 224-236.
18. Meskins MS & Bidlack WR (2006) Nutrient-gene interactions. Lavoisier 2000-2007 http://www.lavoisier.fr/notice/gb282010.html
19. Daniel H (2002) Genomics and proteomics: Importance for the future of nutrition research. Br J Nutr 87, S305-S311.
20. Hardenbol P, Baner J, Jain M, et al. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 21, 673-678.
21. Bonetta L (2006) Genome sequencing in the fast lane. Nat Methods 3, 141-147.
22. Dove A (2005) The SNPs are down: Genotyping for the rest of us. Nat Methods 2, 989-994.
23. Herr A, Grutzmann R, Matthaei A, Artelt J, Schrock E, Rump A & Pilarsky C (2005) High-resolution analysis of chromosomal imbalances using the Affymetrix 10K SNP genotyping chip. Genomics 85, 392-400.
24. Elahi E & Ronaghi M (2004) Pyrosequencing; a tool for DNA sequencing analysis. Methods Mol Biol 255, 211-220.
25. Frigo DE, Bich ND, Melnik LI, Schief LS, Collins-Burow BM, Pace DK, McLachlan JA & Burow ME (2002) Flavonoid phytochemicals regulate activator protein-1 signal transduction pathways in endometrial and kidney stable cell lines1. J Nutr 132, 1848-1853.
26. Gross-Steinmeyer K, Stapleton PL, Liu F, et al. (2004) Phytochemical-induced changes in gene expression of carcinogen-metabolizing enzymes in cultured human primary hepatocyt. Xenobiotica 34, 7, 619-632.
27. Gallou-Kabani C, Vigé A, Gross MS & Junien C (2007) Nutri-epigenomics: Lifelong remodelling of our epigenomes by nutritional and metabolic factors and betone. Clin Chem Lab Med 3, 321-327.
28. Laird PW (2005) Cancer epigenetics. Hum Mol Genet 14, R65-R76.
29. Velculescu VE, Zhang L, Vogelstein B & Kinzler KW, (1995) Serial analysis of gene expression. Science 270, 484-487.
30. Matsumura H, Nasir KHB, Yoshida, K, Ito A, Kahl G, Krüger DH & Terauchi R (2006) SuperSAGE array: The direct use of 26-base-pair transcript tags in oligonucleotide arrays. Nat Methods 3, 421.
31. Christen Y, Olano-Martin E & Packer L (2002) Egb 761 in the postgenomic era: New tools from molecular biology for the study of complex products such as Ginkgo biloba extract. Cell Mol Biol 48, 539.
32. Rice L, Handayani R, Cui Y, Medrano T, Von Samedi, Baker H, Szabo NJ, Romet CHJ, Goodison S & Shiverick KT (2007) Soy isoflavones exert differential effects on androgen responsive genes in LNCaP human prostate canrer cells. J Nutr 137, 964-912.
33. De Longueville F, Atienzar FA, Marcq L, et al. (2003) Use of a low-density microarray for studying gene expression patterns induced by hepatotoxicants on primary cultures of rat hepatocytes. Toxicol Sci 75, 378-392.
34. Montgomery MK (2004) RNA interference: Historical overview and significance. Methods Mol Biol 265, 3-21.
35. Grunweller A & Hartmann RK (2005) RNA interference as a gene-specific approach for molecular medicine. Curr Med Chem 12, 3143-3161.
36. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS & Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773.
37. Barad O, Meiri E, Avniel A, et al. (2004) MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues. Genome Res 14, 2486-2494.
38. Lu J, Getz G, Miska EA, et al. (2005) MicroRNA expression profiles classify human cancers. Nature 435, 834-839.
39. Camunins JM, He Y, Leary RJ, et al. (2006) The colorectal microRNAome. Proc Natl Acad Sci USA 103, 3687-3692.
40. Poy MN, Eliasson L, Krutzfeldt J, et al. (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432 226-230.
41. Kim H, Page GP & Barnes S (2004) Proteomics and mass spectrometry in nutrition research. Nutrition 20, 155-165.
42. Ping P, Vondriska TM, Creighton CJ, et al. (2005) A functional annotation of subprotomes in human plasma. Proteomics 5, 3506-3519.
43. Schweigert FJ (2007) Nutritional proteomics methods and concepts for research in nutritional science. Ann Nutr Metab 51, 99-407.
44. Wang J, Li D, Dangott LJ & Wuy G (2006) Proteomics and its role in nutrition research. J Nutr 136, 1759-1762.
45. Fuchs D, Winkelmann I, Johnson IT, Mariman E, Wenzel U & Daniel H (2005) Proteomics in nutrition research: Principles, technologies and applications. Br J Nutr 94, 302-314.
46. Smith L (2006) Proteomics: Challenges and emerging technologies. Expert Rev Proteomics 3, 6, 573-577.
47. Mouat MF, Kolli K, Orlando R, Hargrgve JL & Grider A (2005) The effects of quercetin on SW480 human colon carcinoma cells: A proteomic study. Nutr J 4, 11.
48. Brooksbarak C (2000) This way up and handle with care. Nat Rev Mol Cell Biol 1, October 2000.
49. Keun HC (2006) Metabonomic modeling of drug toxicity. Pharmacol Ther 109, 92-106.
50. Quackenbush J (2006) From 'omes' to biology. Anim Genet 37, Suppl. 1, 48-56.
51. Rist MJ, Wenzel U & Daniel H (2006) Nutrition and food science go genomic. Trends Biotechnol 24, 4, 172-178.
52. Solanky KS, Bailey NJ, Beckwith-Hall BM, Davis A, Bingham S, Holmes E, Nicholson JK & Cassidy A (2003) Application of biofluid 1H nuclear magnetic resonance-based metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal Biochem 323, 197-204.
53. Bailey NJ, Stanley PD, Hadfield ST, Lindon JC & Nicholson JK (2000) Mass spectrometrically detected directly coupled high performance liquid chromatography/nuclear magnetic resonance spectroscopy/mass spectrometry for the identification of xenobiotic metabolites in maize plants. Rapid Commun Mass Spectrom 14, 679-684.
54. Halket JM, Przyborowska A, Stein SE, Mallard WG, Down S & Chalmers RA (1999) Deconvolution gas chromatography/mass spectrometry of urinary organic acids - potential for pattern recognition and automated identification of metabolic disorders. Rapid Commun Mass Spectrom 13, 279-284.
55. Choi YH, Tapias EC, Kim HK, Lefeber AWM, Erkelens C, Verhoeven, JTJ, Brzin J, Zel J & Verpoorte R (2004) Metabolic discrimination of Catharanthus roseus leaves infected by Phytoplasma using 1H-NMR spectroscopy and multivariate data analysis. Plant Physiol 135 2398-2410.
56. Dunn WB & Ellis DI (206) Metabolomics: Current analytical platforms and methodologies. Trends Analyt Chem 24, 4, 285-294.
57. Katajamaa M & Orešič M (2005) Processing methods for differential analysis of LC/MS profile data http://www.biomedcentral.com/content/pdf/1471-2105-6-179.pdf
58. Jansen JJ, Hoefsloot HCJ, Boelens HFM, Van der Greef J & Smilde AK (2004) Analysis of longitudinal metabolomics data. Bioinformatics 20, 15, 2438-2446.
59. Kohonen T (1982) Self-organized formation of topologically correct feature maps. Biol Cybern 43, 59-69.
60. Wolf D, Gray CP & de Saizieu A (1000) Visualising gene expression in its metabolic context. Brief Bioinform 1, 297-304.
61. Mendes P (2002) Emerging bioinformatics for the metabolome. Brief Bioinform 3, 134-145.
62. Seger CH & Sturm S (2007) Analytical aspects of plant metabolite profiling platforms: Current standings and future aims. J Proteome Res 6, 480-497.
63. Wishart DS, Tzur D, Knox C, et al. (2007) HMDB: The Human Metabolome Database. Nucleic Acids Res 35, Database issue, D521-D526.
64. Gibney MJ, Walsh M, Brennan L, Roche HM, German B & Van Ommen B (2005) Metabolomics in human nutrition: Opportunities and challenges. Am J Clin Nutr 82, 497-503.
65. Young VR (2002) 2001 W.O. Atwater Memorial Lecture and the 2001 ASNS President's Lecture: Human Nutrient Requirements. The challenge of the Post Genome Era. J Nutr 132, 621-629.