Omics and its potential impact on R&D and regulation of complex herbal products

Journal of Ethnopharmacology

Volumn 140, Issue 3, 2012, Pages 587-593

  Pelkonen, Olavi ^a   Pasanen, Markku ^b   Lindon, John C ^c   Chan, Kelvin ^d,e   Zhao, Liping ^f   Deal, Greer ^g   Xu, Qihe ^h   Fan, Tai Ping ⁱ  

^a UNIVERSITY OF OULU   (Finland)

^b UNIVERSITY OF EASTERN FINLAND   (Finland)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF SYDNEY   (Australia)

^e UNIVERSITY OF WESTERN SYDNEY   (Australia)

^f Shanghai Jiao Tong University   (China)

^g Global Regulatory Services   (United Kingdom)

^h KING'S COLLEGE LONDON   (United Kingdom)

ⁱ UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Chinese herbal medicine; Future perspectives; Omics in drug development; Regulation of pharmaceuticals; Systems biology

Indexed keywords

ABACAVIR; BIOLOGICAL MARKER; CARBAMAZEPINE; CLOPIDOGREL; DASATINIB; ERLOTINIB; FULVESTRANT; GEFITINIB; HERBACEOUS AGENT; LAPATINIB; MARAVIROC; NELFINAVIR; NILOTINIB; PHENYTOIN; TAMOXIFEN; TRASTUZUMAB;

BIOLOGICAL ACTIVITY; CHEMICAL COMPOSITION; CHINESE MEDICINE; DRUG EFFICACY; DRUG INDUSTRY; DRUG SAFETY; HUMAN; HYPERSENSITIVITY REACTION; IN VITRO STUDY; IN VIVO STUDY; PHARMACODYNAMICS; PHARMACOGENOMICS; REVIEW; SYSTEMS BIOLOGY;

CHANDIPURA VIRUS;

EID: 84863393856     PISSN: 03788741     EISSN: 18727573     Source Type: Journal    
DOI: 10.1016/j.jep.2012.01.035     Document Type: Article

References (59)

1. Ainsworth, C., 2011. Networking for new drugs. Nature Medicine 17, 1166-1168.
2. Bilello, J.A., 2005. The agony and ecstasy of omic technologies in drug development. Current Molecular Medicine 5, 39-52. (Pubitemid 40352873)
3. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., et al., 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nature Genetics 29, 365-371. (Pubitemid 34326681)
4. Bylesjö, M., Eriksson, D., Kusano, M., Moritz, T., Trygg, J., 2007. Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. Plant Journal 52, 1181-1191. (Pubitemid 350237582)
5. Chan, E.C., Yap, S.L., Lau, A.J., Leow, P.C., Toh, D.F., Koh, H.L., 2007. Ultra-performance liquid chromatography/time-of-flight mass spectrometry based metabolomics of raw and steamed Panax notoginseng. Rapid Communications in Mass Spectrometry 21, 519-528. (Pubitemid 46294300)
6. Chan, K., 1995. Progress in traditional Chinese medicine. Trends in Pharmacological Sciences 16, 182-187.
7. Chen, C., Gonzalez, F.J., Idle, J.R., 2007. LC-MS-based metabolomics in drug metabolism. Drug Metabolism Reviews 39, 581-597. (Pubitemid 47355739)
8. Chen, C., Krausz, K.W., Idle, J.R., Gonzalez, F.J., 2008a. Identification of novel toxicity-associated metabolites by metabolomics and mass isotopomer analysis of acetaminophen metabolism in wild-type and Cyp2e1-null mice. Journal of Biological Chemistry 283, 4543-4559.
9. Chen, M., Ni, Y., Duan, H., Qiu, Y., Guo, C., Jiao, Y., Shi, H., Su, M., Jia, W., 2008b. Mass spectrometry-based metabolic profiling of rat urine associated with general toxicity induced by the multiglycoside of Tripterygium wilfordii Hook. f. Chemical Research in Toxicology 21, 288-294.
10. Cho, J.Y., Kang, D.W., Ma, X., Ahn, S.H., Krausz, K.W., Luecke, H., Idle, J.R., Gonzalez, F.J., 2009. Metabolomics reveals a novel vitamin E metabolite and attenuated vitamin E metabolism upon PXR activation. Journal of Lipid Research 50, 924-937.
11. Clayton, T.A., Baker, D., Lindon, J.C., Everett, J.R., Nicholson, J.K., 2009. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proceedings of National Academy of Sciences USA 106, 14728-14733.
12. Clayton, T.A., Lindon, J.C., Cloarec, O., Antti, H., Charuel, C., Hanton, G., Provost, J.-P., Le Net, J.-L., Baker, D., Walley, R.J., Everett, J.R., Nicholson, J.K., 2006. Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature 440, 1073-1077.
13. Collins, F.S., 2011. Reengineering translational science: the time is right. Science Translational Medicine 3, 90cm17.
14. Dieterle, F., Sistare, F., Goodsaid, F., Papaluca, M., Ozer, J.S., Webb, C.P., et al., 2010. Renal biomarker qualification submission: a dialog between the FDA-EMEA and Predictive Safety Testing Consortium. Nature Biotechnology 28, 455-462.
15. Fardet, A., Llorach, R., Orsoni, A., Martin, J.F., Pujos-Guillot, E., Lapierre, C., Scalbert, A., 2008. Metabolomics provide new insight on the metabolism of dietary phytochemicals in rats. Journal of Nutrition 138, 1282-1287.
16. Guo, L., Li, Q., Xia, Q., Dial, S., Chan, P.C., Fu, P., 2009. Analysis of gene expression changes of drug metabolizing enzymes in the livers of F344 rats following oral treatment with kava extract. Food and Chemical Toxicology 47, 433-442.
17. Guo, L., Shi, Q., Dial, S., Xia, Q., Mei, N., Li, Q.Z., Chan, P.C., Fu, P., 2010. Gene expression profiling in male B6C3F1 mouse livers exposed to kava identifies - changes in drug metabolizing genes and potential mechanisms linked to kava toxicity. Food and Chemical Toxicology 48, 686-696.
18. Hamburg, M.A., 2011. Advancing regulatory science. Science 331, 987 (Editorial).
19. Holmes, E., Tang, H., Wang, Y., Seger, C., 2006. The assessment of plant metabolite profiles by NMR-based methodologies. Planta Medica 72, 771-785. (Pubitemid 44204639)
20. Holmes, E., Li, J.V., Athanasiou, T., Ashrafian, H., Nicholson, J.K., 2011. Understanding the role of gut microbiome-host metabolic signal disruption in health and disease. Trends in Microbiology 19, 349-359.
21. Hu, Y.F., Kaplow, J., He, Y., 2005. From traditional biomarkers to transcriptome analysis in drug development. Current Molecular Medicine 5, 29-38. (Pubitemid 40352872)
22. Jiang, M., Yang, J., Zhang, C., Liu, B., Chan, K., Cao, H., Lu, A., 2010. Clinical studies with traditional Chinese medicine in the past decade and future research and development. Planta Medica 76, 2048-2064.
23. Jiang, M., Zhang, C., Cao, H., Chan, K., Lu, A., 2011. The role of Chinese medicine in the treatment of chronic diseases in China. Planta Medica 77, 873-881.
24. Kang, Y.J., 2008. Herbogenomics: from traditional Chinese medicine to novel therapeutics. Experimental Biological Medicine 233, 1059-1065.
25. Kinross, J.M., Holmes, E., Darzi, A.W., Nicholson, J.K., 2011. Metabolic phenotyping in monitoring of surgical patients. Lancet 377, 1817-1819.
26. Lam, W., Bussom, S., Guan, F., Jiang, Z., Zhang, W., Gullen, E.A., Liu, S.H., Cheng, Y.C., 2010. The four-herb Chinese medicine PHY906 reduces chemotherapy-induced gastrointestinal toxicity. Science Translational Medicine 2, 45ra59.
27. Leighton, J.K., 2005. Application of emerging technologies in toxicology and safety assessment: regulatory perspectives. International Journal of Toxicology 24, 153-155. (Pubitemid 40993363)
28. Leighton, J.K., Brown, P., Ellis, A., Harlow, P., Harrouk, W., Pine, P.S., Robison, T., Rosario, L., Thompson, K., 2006. Workgroup report: Review of genomics data based on experience with mock submissions-view of the CDER Pharmacology Toxicology Nonclinical Pharmacogenomics Subcommittee. Environmental Health Perspectives 114, 573-578.
29. Li, W., Deng, Y., Dai, R., Yu, Y., Saeed, M.K., Li, L., Meng, W., Zhang, X., 2007. Chromatographic fingerprint analysis of Cephalotaxus sinensis from various sources by high-performance liquid chromatography-diodearray detection-electrospray ionization-tandem mass spectrometry. Journal of Pharmaceutical and Biomedical Analysis 45, 38-46. (Pubitemid 47374997)
30. Lindon, J.C., Keun, H.C., Ebbels, T.M.D., Pearce, J.M.T., Holmes, E., Nicholson, J.K., 2005. The Consortium for Metabonomic Toxicology (COMET): aims, activities and achievements. Pharmacogenomics 6, 691-699. (Pubitemid 41479414)
31. Liu, A., Chen, Y., Yang, Z., Feng, Y., Rui, W., Luo, W., Liu, Y., Gonzalez, F.J., Dai, R., 2009a. New metabolites of fenofibrate in Sprague-Dawley rats by UPLC-ESI-QTOF-MS-based metabolomics coupled with LC-MS/MS. Xenobiotica 39, 345-354.
32. Liu, A., Patterson, A.D., Yang, Z., Zhang, X., Liu, W., Qiu, F., Sun, H., Krausz, K.W., Idle, J.R., Gonzalez, F.J., Dai, R., 2009b. Fenofibrate metabolism in the cynomolgus monkey using ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry-based metabolomics. Drug Metabolism and Disposition 37, 1157-1163.
33. Lu, A., Jiang, M., Zhang, C., Chan, K., 2011. An integrative approach of linking traditional Chinese medicine pattern classification and biomedical diagnosis. Journal of Ethnopharmacology, doi:10.1016/j.jep.2011.08.045.
34. Ma, C., Wang, H., Lu, X., Xu, G., Liu, B., 2008. Metabolic fingerprinting investigation of Artemisia annua L. in different stages of development by gas chromatography and gas chromatography-mass spectrometry. Journal of Chromatography A 1186, 412-419. (Pubitemid 351375211)
35. MacGregor, J.T., 2003. The future of regulatory toxicology: impact of the biotechnology revolution. Toxicological Science 75, 236-248. (Pubitemid 37220271)
36. Nicholson, J.K., Wilson, I.D., Lindon, J.C., 2011. Pharmacometabonomics as an effector for personalized medicine. Pharmacogenomics 12, 103-111.
37. Qiu, J., 2007. 'Back to the future' for Chinese herbal medicines. Nature Reviews in Drug Discovery 6, 506-507. (Pubitemid 47019438)
38. Ross, J.S., Slodkowska, E.A., Symmans, W.F., Pusztai, L., Ravdin, P.M., Hortobagyi, G.N., 2009. The HER-2 receptor and breast cancer: ten years of targeted anti-HER-2 therapy and personalized medicine. Oncologist 14, 320-368.
39. Sansone, S.A., Fan, T., Goodacre, R., Griffin, J.L., Hardy, N.W., Kaddurah-Daouk, R., et al., 2007. The metabolomics standards initiative. Nature Biotechnology 25, 846-848.
40. Siest, G., Marteau, J.-B., Visvikis-Siest, S., 2009. Personalized therapy and pharmacogenomics: future perspective. Pharmacogenomics 10, 927-930.
41. Sim, S.C., Ingelman-Sundberg, M., 2011. Pharmacogenomic biomarkers: new tools in current and future drug therapy. Trends in Pharmacological Sciences 32, 72-81.
42. Sun, B., Wu, S., Li, L., Li, H., Zhang, Q., Chen, H., et al., 2009a. A metabolomic analysis of the toxicity of Aconitum sp. alkaloids in rats using gas chromatography/mass spectrometry. Rapid Communications in Mass Spectrometry 23, 1221-1228.
43. Sun, J., Von Tungeln, L.S., Hines, W., Beger, R.D., 2009b. Identification of metabolite profiles of the catechol-O-methyl transferase inhibitor tolcapone in rat urine using LC/MS-based metabonomics analysis. Journal of Chromatography B 877, 2557-2565.
44. Sun, J., Schnackenberg, L.K., Beger, R.D., 2009. Studies of acetaminophen and metabolites in urine and their correlations with toxicity using metabolomics. Drug Metabolism Letters 3, 130-136.
45. Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian Jr., R.K, Jones, A.R., et al., 2007. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology 25, 887-893. (Pubitemid 47236919)
46. Tilton, R., Paiva, A.A., Guan, J.Q., Marathe, R., Jiang, Z., van Eyndhoven, W., et al., 2010. A comprehensive platform for quality control of botanical drugs (PhytomicsQC): A case study of Huangqin Tang (HQT) and PHY906. Chinese Medicine August (5), 30.
47. van der Greef, J., van Wietmarschen, H., Schroen, J., Wang, M., Hankemeier, T., Xu, G., 2010. Systems biology-based diagnostic principles as pillars of the bridge between Chinese and Western medicine. Planta Medica 76, 2036-2047.
48. van Velzen, E.J., Westerhuis, J.A., van Duynhoven, J.P., van Dorsten, F.A., Grün, C.H., Jacobs, D.M., Duchateau, G.S., Vis, D.J., Smilde, A.K., 2009. Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites. Journal of Proteome Research 8, 3317-3330.
49. Wang, M., Lamers, R.J., Korthout, H.A., van Nesselrooij, J.H., Witkamp, R.F., van der Heijden, R., et al., 2005. Metabolomics in the context of systems biology: bridging traditional Chinese medicine and molecular pharmacology. Phytotherapy Research 19, 173-182. (Pubitemid 40827637)
50. Wang, X., Lv, H., Sun, H., Liu, L., Yang, B., Sun, W., Wang, P., Zhou, D., Zhao, L., Dou, S., Zhang, G., Cao, H., 2008. Metabolic urinary profiling of alcohol hepatotoxicity and intervention effects of Yin Chen Hao Tang in rats using ultra-performance liquid chromatography/electrospray ionization quadruple time-of-flight mass spectrometry. Journal of Pharmaceutical and Biomedical Analysis 48, 1161-1168.
51. Wang, X., Su, M., Qiu, Y., Ni, Y., Zhao, T., Zhou, M., et al., 2007. Metabolic regulatory network alterations in response to acute cold stress and ginsenoside intervention. Journal of Proteome Research 6, 3449-3455. (Pubitemid 47522735)
52. Wang, Y., Tang, H., Nicholson, J.K., Hylands, P.J., Sampson, J., Whitcombe, I., et al., 2004. Metabolomic strategy for the classification and quality control of phytomedicine: a case study of chamomile flower (Matricaria recutita L.). Planta Medica 70, 250-255. (Pubitemid 38445192)
53. Wang, J., van der Heijden, R., Spruit, S., Hankermeier, T., Chan, K., van der Greef, J., Xu, G., Wang, M., 2009. Quality and safety of Chinese herbal medicines guided by a systems biology perspective. Journal of Ethnopharmacology 126, 31-41.
54. Xie, G., Plumb, R., Su, M., Xu, Z., Zhao, A., Qiu, M., Long, X., Liu, Z., Jia, W., 2008. Ultraperformance LC/TOF MS analysis of medicinal Panax herbs for metabolomic research. Journal of Separation Science 31, 1015-1026. (Pubitemid 351649827)
55. Xie, G., Ye, M., Wang, Y., Ni, Y., Su, M., Huang, H., Qiu, M., Zhao, A., Zheng, X., Chen, T., Jia, W., 2009. Characterization of pu-erh tea using chemical and metabolic profiling approaches. Journal of Agricultural and Food Chemistry 57, 3046-3054.
56. Xue, T., Roy, R., 2003. Studying traditional Chinese medicine. Science 300, 740-741.
57. Zhang X, Zhao Y, Hu Y, Liu P, Zhao L., 2011. Gut microbiota-targeted, whole-body systems biology for understanding traditional Chinese medicine. 13, 202-212.
58. Zhao, L., Shen, J., 2010. Whole-body systems approaches for gut microbiota-targeted, preventive healthcare. Journal of Biotechnology 149, 183-190.
59. Zhao, X., Zhang, Y., Meng, X., Yin, P., Deng, C., Chen, J., Wang, Z., Xu, G., 2008. Effect of a traditional Chinese medicine preparation Xindi soft capsule on rat model of acute blood stasis: a urinary metabonomics study based on liquid chromatography-mass spectrometry. Journal of Chromatography B 873, 151-158.