DNA Microarray-Based Screening and Characterization of Traditional Chinese Medicine

Abstract

The application of DNA microarray assay (DMA) has entered a new era owing to recent innovations in omics technologies. This review summarizes recent applications of DMA-based gene expression profiling by focusing on the screening and characterizationof traditional Chinese medicine. First, herbs, mushrooms, and dietary plants analyzed by DMA along with their effective components and their biological/physiological effects are summarized and discussed by examining their comprehensive list and a list of representative effective chemicals. Second, the mechanisms of action of traditional Chinese medicine are summarized by examining the genes and pathways responsible for the action, the cell functions involved in the action, and the activities found by DMA (silent estrogens). Third, applications of DMA for traditional Chinese medicine are discussed by examining reported examples and new protocols for its use in quality control. Further innovations in the signaling pathway based evaluation of beneficial effects and the assessment of potential risks of traditional Chinese medicine are expected, just as are observed in other closely related fields, such as the therapeutic, environmental, nutritional, and pharmacological fields.

Keywords: DNA microarray; estrogen; food chemicals; signaling pathway; traditional Chinese medicine.

Figure 1

Summary of actions and their mechanisms by the chemicals related to traditional Chinese medicine. The mechanisms of action by the chemicals originally identified or isolated from medicinal herbs, mushrooms and dietary plants (aculeatin, brefeldin A, ergosterol peroxide, grifolin, β-hydroxyisovalerylshikonin, paeonol, quercetin and tanshinone IIA) within the cytosol (blue area) or the nucleus (yellow area) are summarized. APP: amyloid precursor protein; CCL2: chemokine (C-C motif) ligand 2; ERK: extracellular-signal-regulated kinase; β-HIVS: β-hydroxyisovalerylshikonin; MAPK: mitogen-activated protein kinase; PPAR-γ: peroxisome proliferator-activated receptor γ; PXR: pregnane X receptor; Rb: retinoblastoma protein; TNFR: tumor necrosis factor receptor; and TRAP1: tumor necrosis factor receptor-associated protein 1.

Figure 2

Quality control of herbal components by gene expression profiling. Examples of application of DMA for quality control of TCM are summarized. (A) A simplified protocol of quality control of herbal extracts. Gene expression profiles for different sources of herbal extracts (A1 to A5) are compared with that of a standard (S) using correlation coefficients (R-values) based on linear regression. A case of deviation (A3) can be detected by comparing R-values for the profiles of the genes appropriately selected. (B) Selection of gene sets for gene expression profiling-based quality control. The degree of stability in quality control can be influenced and controlled by selecting arbitrarily grouped genes (G1 to G3), which show stable (G1), less stable (G2) or unstable (G3) reproducibility upon comparing various lots (A1 and A2) of the herbal extracts with a standard (S). (C) Selection of gene sets for gene function-based quality control. The profiling shown in (B) can be performed with functionally grouped genes (F1 to F3) to give a protocol of efficacy-based quality control of herbal extracts.