Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis

Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and... The discovery of new anti-inflammatory drugs is often based on an interaction with a specific target, although other pathways often play a primary or secondary role. Anti-inflammatory drugs can be categorized into classes, based on their mechanism of action. In this article we investigate the possibility to characterize novel anti-inflammatory compounds by three holistic methods. For this purpose, we make use of macrophage-like U937 cells which are stimulated with LPS in the absence or presence of an anti-inflammatory compound. Using micro-arrays, 2-D gel electrophoresis and a LC-MS method for lipids the effects on the transcriptome, proteome and metabolome of the exposed cells is investigated. The expression patterns are subsequently analyzed using in-house developed pattern recognition tools. Using the methods described above, we have examined the effects of six anti-inflammatory compounds. Our results demonstrate that different classes of anti-inflammatory compounds show distinct and characteristic mRNA, protein, and lipid expression patterns, which can be used to categorise known molecules and to discover and classify new leads. The potential of our approach is illustrated by the analysis of several beta (2)-adrenergic agonists (β 2 -agonists). In addition to their primary pharmacological target, β 2 -agonists posses certain anti-inflammatory properties. We were able to show that zilpaterol, a poorly characterized β 2 -agonist, gives rise to an almost identical expression pattern as the β 2 -agonists clenbuterol and salbutamol. Furthermore we have identified specific mRNA, protein and lipid markers for the anti-inflammatory compounds investigated in this study. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png International Immunopharmacology Elsevier

Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis

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Publisher
Elsevier
Copyright
Copyright © 2004 Elsevier B.V.
ISSN
1567-5769
eISSN
1878-1705
DOI
10.1016/j.intimp.2004.07.008
Publisher site
See Article on Publisher Site

Abstract

The discovery of new anti-inflammatory drugs is often based on an interaction with a specific target, although other pathways often play a primary or secondary role. Anti-inflammatory drugs can be categorized into classes, based on their mechanism of action. In this article we investigate the possibility to characterize novel anti-inflammatory compounds by three holistic methods. For this purpose, we make use of macrophage-like U937 cells which are stimulated with LPS in the absence or presence of an anti-inflammatory compound. Using micro-arrays, 2-D gel electrophoresis and a LC-MS method for lipids the effects on the transcriptome, proteome and metabolome of the exposed cells is investigated. The expression patterns are subsequently analyzed using in-house developed pattern recognition tools. Using the methods described above, we have examined the effects of six anti-inflammatory compounds. Our results demonstrate that different classes of anti-inflammatory compounds show distinct and characteristic mRNA, protein, and lipid expression patterns, which can be used to categorise known molecules and to discover and classify new leads. The potential of our approach is illustrated by the analysis of several beta (2)-adrenergic agonists (β 2 -agonists). In addition to their primary pharmacological target, β 2 -agonists posses certain anti-inflammatory properties. We were able to show that zilpaterol, a poorly characterized β 2 -agonist, gives rise to an almost identical expression pattern as the β 2 -agonists clenbuterol and salbutamol. Furthermore we have identified specific mRNA, protein and lipid markers for the anti-inflammatory compounds investigated in this study.

Journal

International ImmunopharmacologyElsevier

Published: Nov 1, 2004

References

  • MAP kinases in the immune response
    Dong, C.; Davis, R.J.; Flavell, R.A.
  • Establishment and characterization of a human histiocytic lymphoma cell line (U-937)
    Sundstrom, C.; Nilsson, K.
  • Hsp70 exerts its anti-apoptotic function downstream of caspase-3-like proteases
    Jaattela, M.; Wissing, D.; Kokholm, K.; Kallunki, T.; Egeblad, M.
  • Heat shock proteins: endogenous modulators of apoptotic cell death
    Garrido, C.; Gurbuxani, S.; Ravagnan, L.; Kroemer, G.
  • Dissociation of apoptosis induction and CD36 upregulation by enzymatically modified low-density lipoprotein in monocytic cells
    Jostarndt, K.; Gellert, N.; Rubic, T.; Weber, C.; Kuhn, H.
  • Lysophosphatidylcholine induces apoptosis in AR42J cells
    Masamune, A.; Sakai, Y.; Satoh, A.; Fujita, M.; Yoshida, M.; Shimosegawa, T.

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