Pathway-focused bioassays and transcriptome analysis contribute to a better activity monitoring of complex herbal remedies
详细信息 查看全文
- 作者：Angela Klein (1)
Oliver A Wrulich (1)
Marcel Jenny (1)
Peter Gruber (1)
Kathrin Becker (1)
Dietmar Fuchs (2)
Johanna M Gostner (1)
Florian überall (1) - 关键词：HepG2 ; Microarray ; Multicomponent ; Pathway analysis ; Polyherbal ; qPCR
- 刊名：BMC Genomics
- 出版年：2013
- 出版时间：December 2013
- 年：2013
- 卷：14
- 期：1
- 全文大小：481KB
- 参考文献：1. Wagner H, Ulrich-Merzenich G: Synergy research: approaching a new generation of phytopharmaceuticals. / Phytomedicine 2009, 16:97-10. med.2008.12.018">CrossRef
2. Schmidt B, Ribnicky DM, Poulev A, Logendra S, Cefalu WT, Raskin I: A natural history of botanical therapeutics. / Metabolism 2008, 57:S3-. metabol.2008.03.001">CrossRef
3. Groten JP, Butler W, Feron VJ, Kozianowski G, Renwick AG, Walker R: An analysis of the possibility for health implications of joint actions and interactions between food additives. / Regul Toxicol Pharmacol 2000, 31:77-1. CrossRef
4. Münzel T, Gori T, Bruno RM, Taddei S: Is oxidative stress a therapeutic target in cardiovascular disease? / Eur Heart J 2010, 31:2741-748. CrossRef
5. Andersen JK: Oxidative stress in neurodegeneration: cause or consequence? / Nat Med 2004, 10:S18-5. CrossRef
6. Chisolm GM, Steinberg D: The oxidative modification hypothesis of atherogenesis: an overview. / Free Radic Biol Med 2000, 28:1815-826. CrossRef
7. Young IS, Woodside JV: Antioxidants in health and disease. / J Clin Pathol 2001, 54:176-86. CrossRef
8. Halliwell B: Antioxidants in human health and disease. / Annu Rev Nutr 1996, 16:33-0. CrossRef
9. Masella R, Di Benedetto R, Varì R, Filesi C, Giovannini C: Novel mechanisms of natural antioxidant compounds in biological systems: involvement of glutathione and glutathione-related enzymes. / J Nutr Biochem 2005, 16:577-86. CrossRef
10. Stevenson DE, Hurst RD: Polyphenolic phytochemicals–just antioxidants or much more? / Cell Mol Life Sci 2007, 64:2900-916. CrossRef
11. Kang KW, Lee SJ, Kim SG: Molecular mechanism of nrf2 activation by oxidative stress. / Antioxid Redox Signal 2005, 7:1664-673. CrossRef
12. Zaknun D, Schroecksnadel S, Kurz K, Fuchs D: Potential role of antioxidant food supplements, preservatives and colorants in the pathogenesis of allergy and asthma. / Int Arch Allergy Immunol 2012, 157:113-24. CrossRef
13. Mennen LI, Walker R, Bennetau-Pelissero C, Scalbert A: Risks and safety of polyphenol consumption. / Am J Clin Nutr 2005, 81:326-29.
14. Dinkova-Kostova AT, Talalay P: Direct and indirect antioxidant properties of inducers of cytoprotective proteins. / Mol Nutr Food Res 2008, 52:S128-38.
15. Sarkar FH, Li Y, Wang Z, Kong D: Cellular signaling perturbation by natural products. / Cell Signal 2009, 21:1541-547. CrossRef
16. Debouck C, Goodfellow PN: DNA microarrays in drug discovery and development. / Nat Genet 1999, 21:48-0. CrossRef
17. Ulrich-Merzenich G, Zeitler H, Jobst D, Panek D, Vetter H, Wagner H: Application of the "-Omic-" technologies in phytomedicine. / Phytomedicine 2007, 14:70-2. med.2006.11.011">CrossRef
18. Gohil K, Chakraborty AA: Applications of microarray and bioinformatics tools to dissect molecular responses of the central nervous system to antioxidant micronutrients. / Nutrition 2004, 20:50-5. CrossRef
19. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. / Nat Genet 2001, 29:365-71. CrossRef
20. Werner T: Bioinformatics applications for pathway analysis of microarray data. / Curr Opin Biotechnol 2008, 19:50-4. CrossRef
21. Efferth T, Koch E: Complex interactions between phytochemicals. The multi-target therapeutic concept of phytotherapy. / Curr Drug Targets 2011, 12:122-32. CrossRef
22. Wink M: Evolutionary advantage and molecular modes of action of multi-component mixtures used in phytomedicine. / Curr Drug Metab 2008, 9:996-009. CrossRef
23. Gostner JM, Wrulich OA, Jenny M, Fuchs D, Ueberall F: An update on the strategies in multicomponent activity monitoring within the phytopharmaceutical field. / BMC Complement Altern Med 2012, 12:18. CrossRef
24. Ulrich-Merzenich G, Panek D, Zeitler H, Wagner H, Vetter H: New perspectives for synergy research with the "omic"-technologies. / Phytomedicine 2009, 16:495-08. med.2009.04.001">CrossRef
25. Hudson J, Altamirano M: The application of DNA micro-arrays (gene arrays) to the study of herbal medicines. / J Ethnopharmacol 2006, 108:2-5. CrossRef
26. Becker K, Klein A, Wrulich OA, Gruber P, Fuchs D, Jenny M, Ueberall F, Gostner JM: Transcriptome analysis in HepG2 cells revealed multiple activity mechanisms of a Tibetan polyherbal formula [abstract]. / Z Phytother 2012, 33:P03. CrossRef
27. / Product Information for Patients. ma.ch/fileadmin/user_upload/pdfs/PB_e/Kapseln/PADMA_28_KAPS_PI_E_0708_290909.pdf" class="a-plus-plus">http://www.padma.ch/fileadmin/user_upload/pdfs/PB_e/Kapseln/PADMA_28_KAPS_PI_E_0708_290909.pdf
28. Drabaek H, Mehlsen J, Himmelstrup H, Winther K: A botanical compound, PADMA-28, increases walking distance in stable intermittent claudication. / Angiology 1993, 44:863-67. CrossRef
29. Melzer J, Brignoli R, Diehm C, Reichling J, Do DD, Saller R: Treating intermittent claudication with Tibetan medicine PADMA 28: does it work? / Atherosclerosis 2006, 189:39-6. CrossRef
30. Knasmüller S, Mersch-Sundermann V, Kevekordes S, Darroudi F, Huber WW, Hoelzl C, Bichler J, Majer BJ: Use of human-derived liver cell lines for the detection of environmental and dietary genotoxicants; current state of knowledge. / Toxicology 2004, 198:315-28. CrossRef
31. Gerets HH, Hanon E, Cornet M, Dhalluin S, Depelchin O, Canning M, Atienzar FA: Selection of cytotoxicity markers for the screening of new chemical entities in a pharmaceutical context: a preliminary study using a multiplexing approach. / Toxicol In Vitro 2009, 23:319-32. CrossRef
32. Murakami C, Hirakawa Y, Inui H, Nakano Y, Yoshida H: Effects of epigallocatechin 3-O-gallate on cellular antioxidative system in HepG2 cells. / J Nutr Sci Vitaminol (Tokyo) 2002, 48:89-4. CrossRef
33. Lee YY, Kim HG, Jung HI, Shin YH, Hong SM, Park EH, Sa JH, Lim CJ: Activities of antioxidant and redox enzymes in human normal hepatic and hepatoma cell line. / Mol Cells 2002, 14:305-11.
34. / Ingenuity? Pathway Analysis (IPA). m/" class="a-plus-plus">http://www.ingenuity.com/
35. Cheng JT: Review: drug therapy in Chinese traditional medicine. / J Clin Pharmacol 2000, 40:445-50. CrossRef
36. Balázsi G, Oltvai ZN: Sensing your surroundings: how transcription-regulatory networks of the cell discern environmental signals. / Sci STKE 2005, 282:pe20. CrossRef
37. Agoston V, Csermely P, Pongor S: Multiple weak hits confuse complex systems: a transcriptional regulatory network as an example. / Phys Rev E Stat Nonlin Soft Matter Phys 2005, 71:051909. CrossRef
38. Kitano H: A robustness-based approach to systems-oriented drug design. / Nat Rev Drug Discov 2007, 6:202-10. CrossRef
39. Wermuth CG: Multitargeted drugs: the end of the "one-target-one-disease" philosophy? / Drug Discov Today 2004, 9:826-27. CrossRef
40. Csermely P, Agoston V, Pongor S: The efficiency of multi-target drugs: the network approach might help drug design. / Trends Pharmacol Sci 2005, 26:178-82. CrossRef
41. Liao H, Banbury LK, Leach DN: Antioxidant activity of 45 Chinese herbs and the relationship with their TCM characteristics. / Evid Based Complement Alternat Med 2008, 5:429-34. m/nem054">CrossRef
42. Suter M, Richter C: Anti- and pro-oxidative properties of PADMA 28, a Tibetan herbal formulation. / Redox Rep 2000, 5:17-2.
43. Ginsburg I, Sadovnik M, Sallon S, Milo-Goldzweig I, Mechoulam R, Breuer A, Gibbs D, Varani J, Roberts S, Cleator E, Singh N: PADMA-28, a traditional tibetan herbal preparation inhibits the respiratory burst in human neutrophils, the killing of epithelial cells by mixtures of oxidants and pro-inflammatory agonists and peroxidation of lipids. / Inflammopharmacology 1999, 7:47-2. CrossRef
44. Riley PA: Free radicals in biology: oxidative stress and the effects of ionizing radiation. / Int J Radiat Biol 1994, 65:27-3. CrossRef
45. Zhao W, Diz DI, Robbins ME: Oxidative damage pathways in relation to normal tissue injury. / Br J Radiol 2007, 80:S23-1. CrossRef
46. Rong J, Tilton R, Shen J, Ng KM, Liu C, Tam PK, Lau AS, Cheng YC: Genome-wide biological response fingerprinting (BioReF) of the Chinese botanical formulation ISF-1 enables the selection of multiple marker genes as a potential metric for quality control. / J Ethnopharmacol 2007, 113:35-4. CrossRef
47. Guengerich FP: Influence of nutrients and other dietary materials on cytochrome P-450 enzymes. / Am J Clin Nutr 1995, 61:651S-658S.
48. Moore LB, Goodwin B, Jones SA, Wisely GB, Serabjit-Singh CJ, Willson TM, Collins JL, Kliewer SA: St. John's wort induces hepatic drug metabolism through activation of the pregnane X receptor. / Proc Natl Acad Sci U S A 2000, 97:7500-502. CrossRef
49. Lin JH: CYP induction-mediated drug interactions: in vitro assessment and clinical implications. / Pharm Res 2006, 23:1089-116. CrossRef
50. Ioannides C: / Cytochromes P450: Role in the metabolism and toxicity of drugs and other xenobiotics. Cambridge: RSC Publishing/UK; 2008.
51. Bjornsson TD, Callaghan JT, Einolf HJ, Fischer V, Gan L, Grimm S, Kao J, King SP, Miwa G, Ni L, Kumar G, McLeod J, Obach RS, Roberts S, Roe A, Shah A, Snikeris F, Sullivan JT, Tweedie D, Vega JM, Walsh J, Wrighton SA: The conduct of in vitro and in vivo drug-drug interaction studies: a Pharmaceutical Research and Manufacturers of America (PhRMA) perspective. / Drug Metab Dispos 2003, 31:815-32. md.31.7.815">CrossRef
52. Guengerich FP, Shimada T: Activation of procarcinogens by human cytochrome P450 enzymes. / Mutat Res 1998, 400:201-13. CrossRef
53. Uno S, Dalton TP, Derkenne S, Curran CP, Miller ML, Shertzer HG, Nebert DW: Oral exposure to benzo[a]pyrene in the mouse: detoxication by inducible cytochrome P450 is more important than metabolic activation. / Mol Pharmacol 2004, 65:1225-237. mol.65.5.1225">CrossRef
54. Androutsopoulos VP, Tsatsakis AM, Spandidos DA: Cytochrome P450 CYP1A1: wider roles in cancer progression and prevention. / BMC Cancer 2009, 19:187. CrossRef
55. Zhang R, Sun J, Ma L, Wu X, Pan G, Hao H, Zhou F, J A, Liu C, Ai H, Shang L, Gao H, Peng Y, Wan P, Wu H, Wang G: Induction of cytochromes P450 1A1 and 1A2 by tanshinones in human HepG2 hepatoma cell line. / Toxicol Appl Pharmacol 2011, 252:18-7. CrossRef
56. Chan WK, Yao G, Gu YZ, Bradfield CA: Cross-talk between the aryl hydrocarbon receptor and hypoxia inducible factor signaling pathways. Demonstration of competition and compensation. / J Biol Chem 1999, 274:12115-2123. CrossRef
57. Puga A, Ma C, Marlowe JL: The aryl hydrocarbon receptor cross-talks with multiple signal transduction pathways. / Biochem Pharmacol 2009, 77:713-22. CrossRef
58. Kung T, Murphy KA, White LA: The aryl hydrocarbon receptor (AhR) pathway as a regulatory pathway for cell adhesion and matrix metabolism. / Biochem Pharmacol 2009, 77:536-46. CrossRef
59. Clark DW, Mitra A, Fillmore RA, Jiang WG, Samant RS, Fodstad O, Shevde LA: NUPR1 interacts with p53, transcriptionally regulates p21 and rescues breast epithelial cells from doxorubicin-induced genotoxic stress. / Curr Cancer Drug Targets 2008, 8:421-30. CrossRef
60. Asher G, Lotem J, Kama R, Sachs L, Shaul Y: NQO1 stabilizes p53 through a distinct pathway. / Proc Natl Acad Sci U S A 2002, 99:3099-104. CrossRef
61. Li C, Hossieny P, Wu BJ, Qawasmeh A, Beck K, Stocker R: Pharmacologic induction of heme oxygenase-1. / Antioxid Redox Signal 2007, 9:2227-239. CrossRef
62. Ferrándiz ML, Devesa I: Inducers of heme oxygenase-1. / Curr Pharm Des 2008, 14:473-86. CrossRef
63. Locksley RM, Killeen N, Lenardo MJ: The TNF and TNF receptor superfamilies: integrating mammalian biology. / Cell 2001, 104:487-01. CrossRef
64. Wajant H, Pfizenmaier K, Scheurich P: Tumor necrosis factor signaling. / Cell Death Differ. 2003, 10:45-5. CrossRef
65. Platanias LC: Mechanisms of type-I- and type-II-interferon-mediated signalling. / Nat Rev Immunol 2005, 5:375-6. CrossRef
66. Saha B, Jyothi Prasanna S, Chandrasekar B, Nandi D: Gene modulation and immunoregulatory roles of interferon gamma. / Cytokine 2010, 50:1-4. CrossRef
67. Ou B, Hampsch-Woodill M, Prior RL: Development and validation of an improved oxygen radical absorbance capacity assay using fluorescein as the fluorescent probe. / J Agric Food Chem 2001, 49:4619-626. CrossRef
68. Jenny M, Santer E, Klein A, Ledochowski M, Schennach H, Ueberall F, Fuchs D: Cacao extracts suppress tryptophan degradation of mitogen-stimulated peripheral blood mononuclear cells. / J Ethnopharmacol 2009, 122:261-67. CrossRef
69. Chou TC, Talalay P: Quantitative analysis of dose-effect relationships: The combined effects of multiple drugs or enzyme inhibitors. / Adv Enzyme Regul 1984, 22:27-5. CrossRef
70. Maglione M, Cardini B, Oberhuber R, Watschinger K, Jenny M, Gostner J, Hermann M, Obrist P, Margreiter R, Pratschke J, Brandacher G, Werner ER: Prevention of lethal murine pancreas ischemia reperfusion injury is specific for tetrahydrobiopterin. / Transpl Int 2012, 25:1084-5. CrossRef
71. Bass DA, Parce JW, Dechatelet LR, Szejda P, Seeds MC, Thomas M: Flow cytometric studies of oxidative product formation by neutrophils: a graded response to membrane stimulation. / J Immunol 1983, 130:1910-917.
72. Wang H, Joseph JA: Quantifying cellular oxidative stress by dichlorofluorescein assay using microplate reader. / Free Radic Biol Med 1999, 27:612-16. CrossRef
73. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J, Bioconductor: Open software development for computational biology and bioinformatics. / Genome Biol 2004, 5:R80. CrossRef
74. Wu Z, Irizarry RA, Gentleman R, Murillo FM, Spencer F: A model based background adjustment for oligonucleotide expression arrays. / J Am Stat Assoc 2004, 99:909-17. CrossRef
75. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. / Bioinformatics 2003, 19:185-93. matics/19.2.185">CrossRef
76. Zlokarnik G, Negulescu PA, Knapp TE, Mere L, Burres N, Feng L, Whitney M, Roemer K, Tsien RY: Quantitation of transcription and clonal selection of single living cells with beta-lactamase as reporter. / Science 1998, 279:84-8. CrossRef
77. Pfaffl MW: A new mathematical model for relative quantification in real-time RT-PCR. / Nucleic Acids Res 2001, 29:e45. CrossRef
78. Cicinnati VR, Shen Q, Sotiropoulos GC, Radtke A, Gerken G, Beckebaum S: Validation of putative reference genes for gene expression studies in human hepatocellular carcinoma using real-time quantitative RT-PCR. / BMC Cancer 2008, 8:350. CrossRef
79. Pfaffl MW, Horgan GW, Dempfle L: Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. / Nucleic Acids Res 2002, 30:e36. CrossRef - 作者单位：Angela Klein (1)
Oliver A Wrulich (1)
Marcel Jenny (1)
Peter Gruber (1)
Kathrin Becker (1)
Dietmar Fuchs (2)
Johanna M Gostner (1)
Florian überall (1)
1. Division of Medical Biochemistry, Innsbruck Medical University, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, Austria
2. Division of Biological Chemistry, Innsbruck Medical University, Center for Chemistry and Biomedicine, Innrain 80-82, Innsbruck, Austria
文摘
Background Transcriptome analysis in combination with pathway-focused bioassays is suggested to be a helpful approach for gaining deeper insights into the complex mechanisms of action of herbal multicomponent preparations in living cells. The polyherbalism based concept of Tibetan and Ayurvedic medicine considers therapeutic efficacy through multi-target effects. A polyherbal Indo-Tibetan preparation, Padma 28, approved by the Swiss drug authorities (Swissmedic Nr. 58436), was applied to a more detailed dissection of mechanism of action in human hepatoma HepG2 cells. Cell-free and cell-based assays were employed to evaluate the antioxidant capacity. Genome-wide expression profiling was done by applying Human Genome U133 Plus 2.0 Affymetrix arrays. Pathway- and network-oriented analysis elucidated the affected biological processes. The results were validated using reporter gene assays and quantitative real-time PCR. Results To reveal the direct radical scavenging effects of the ethanolic extract of the Indo-Tibetan polyherbal remedy Padma 28, an in vitro oxygen radical absorbance capacity assay (ORAC) was employed, which resulted in a peroxyl-radical scavenging activity of 2006 ± 235 μmol TE/g. Furthermore, the antioxidant capacity of Padma 28 was analysed in living HepG2 cells, by measuring its scavenging potential against radical induced ROS. This formulation showed a considerable antioxidant capacity by significantly reducing ROS levels in a dose-dependent manner. Integrated transcriptome analysis revealed a major influence on phase I and phase II detoxification and the oxidative stress response. Selected target genes, such as heme oxygenase 1, were validated in qPCR experiments. Network analysis showed 18 interrelated networks involved in important biological functions such as drug and bio-molecule metabolism, molecular transport and cellular communication. Some molecules are part of signaling cascades that are active during development and morphogenesis or are involved in pathological conditions and inflammatory response. Conclusions The identified molecular targets and pathways suggest several mechanisms that underlie the biological activity of the preparation. Although extrapolation of these findings to the in vivo situation is not possible, the results obtained might be the basis for further investigations and new hypotheses to be tested. This study demonstrates the potential of the combination of focused and unbiased research strategies in the mode of action analysis of multicomponent herbal mixtures.