Identification of common or distinct genes related to antitumor activities of a medicinal herb and its major component by oligonucleotide microarray

Comparison of anti-inflammatory effects of berberine, and its natural oxidative and reduced derivatives from Rhizoma Coptidis in vitro and in vivo

BACKGROUND

Berberine (BBR) is the most abundant and major active constituent of Rhizoma Coptidis (RC), which has been widely used to treat inflammatory diseases in traditional oriental medicine. Despite BBR has been found to exhibit pronounced anti-inflammatory effect, the anti-inflammatory activities of its natural derivatives were sparsely dissected out.

PURPOSE

To comparatively investigate the anti-inflammatory potential of BBR, and its natural oxoderivative (oxyberberine, OBB) and reduced derivative (dihydroberberine, DHBB) in vitro and in vivo, and delineate the possible underlying mechanism.

METHODS

LC-MS/MS was used to identify the natural derivatives of BBR in RC. The potential anti-inflammatory properties of BBR and its natural derivatives were comparatively evaluated in vitro by lipopolysaccharide (LPS)-induced RAW264.7 macrophages cells, and in vivo via three typical acute inflammation murine models. Some important inflammation-related molecules were analyzed by ELISA, qRT-PCR and Western blotting.

RESULTS

LC-MS/MS led to the identification of BBR, OBB and DHBB in RC ethyl acetate extract. The in vitro assay indicated that BBR, OBB and DHBB (1.25, 2.5 and 5 μM) pretreatment significantly decreased the levels of pro-inflammatory cytokines tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), prostaglandinE2 (PGE₂) and nitricoxide (NO), and inhibited the mRNA expressions of cyclooxygenase-2 (COX-2) and inducible nitricoxide synthase (iNOS) in a dose-dependent manner, with relative efficiency of OBB > BBR > DHBB. Furthermore, OBB, BBR and DHBB remarkably inhibited the phosphorylation of nuclear factor-κB (NF-κB) p65 and inhibitory kappa Bα (IκBα). In vivo, BBR (20 mg/kg) and OBB (5, 10, and 20 mg/kg) pretreatment significantly ameliorated the xylene-induced ear edema, carrageenan-stimulated paw edema, and acetic acid-elicited vascular permeability in mice in a dose-dependent manner, with OBB exhibiting superior anti-inflammatory effect at the same dose (20 mg/kg). Histopathological analysis indicated that OBB and BBR could markedly attenuate the inflammatory deterioration and decrease the cellular infiltration in paw tissues. Additionally, the carrageenan-induced increases in TNF-α, IL-6, IL-1β, PGE₂ and NO productions, and COX-2 and iNOS mRNA expressions were effectually and concentration-dependently suppressed by OBB and BBR pretreatment.

CONCLUSION

The anti-inflammatory activity of BBR and its natural derivatives was in the order of OBB > BBR > DHBB. OBB was for the first time found to be endowed with pronounced anti-inflammatory property, which was probably associated with suppressing the activation of NF-κB signaling pathway, and the subsequent gene expressions and productions of pro-inflammatory mediators. The results might contribute to illuminating the pharmacodynamic underpinnings of RC and provide evidence for developing OBB as a safe and promising natural lead compound in inflammation treatment.

Coptisine-induced inhibition of Helicobacter pylori: elucidation of specific mechanisms by probing urease active site and its maturation process

In this study, we examined the anti-Helicobactor pylori effects of the main protoberberine-type alkaloids in Rhizoma Coptidis. Coptisine exerted varying antibacterial and bactericidal effects against three standard H. pylori strains and eleven clinical isolates, including four drug-resistant strains, with minimum inhibitory concentrations ranging from 25 to 50 μg/mL and minimal bactericidal concentrations ranging from 37.5 to 125 μg/mL. Coptisine’s anti-H. pylori effects derived from specific inhibition of urease in vivo. In vitro, coptisine inactivated urease in a concentration-dependent manner through slow-binding inhibition and involved binding to the urease active site sulfhydryl group. Coptisine inhibition of H. pylori urease (HPU) was mixed type, while inhibition of jack bean urease was non-competitive. Importantly, coptisine also inhibited HPU by binding to its nickel metallocentre. Besides, coptisine interfered with urease maturation by inhibiting activity of prototypical urease accessory protein UreG and formation of UreG dimers and by promoting dissociation of nickel from UreG dimers. These findings demonstrate that coptisine inhibits urease activity by targeting its active site and inhibiting its maturation, thereby effectively inhibiting H. pylori. Coptisine may thus be an effective anti-H. pylori agent.

Biological-Profiling-Based Systematic Analysis of Rhizoma Coptidis from Different Growing Regions and Its Anticholesterol Biosynthesis Activity on HepG2 Cells

Rhizoma Coptidis is a widely cultivated traditional Chinese herb. Although the chemical profiles of Rhizoma Coptidis have been established previously, the biological profiling of Rhizoma Coptidis has not been conducted yet. In this study, we collected Rhizoma Coptidis varieties from four distinct growing regions and performed genome-wide biological response fingerprinting (BioReF) on HepG2 cells using a gene expression array. Similar biological pathways were affected by extracts of all four Rhizoma Coptidis varieties but not by their analogue, Mahoniae Caulis. Among these pathways, the terpenoid backbone biosynthesis pathway was highly enriched, and six genes in the mevalonate (MVA) pathway were all down-regulated. However, the expression, maturation, as well as the specific DNA binding capacity of their coordinate transcription factor, sterol response element binding protein 2 (SREBP2), was not affected by Rhizoma Coptidis extract (RCE) or its typical active alkaloid berberine. Cellular cholesterol content tests further verified the cholesterol-lowering function of RCE in vitro, which supplements evidence for the use of Rhizoma Coptidis in hyperlipidemia treatment. This is the first described example of evaluating the quality of Rhizoma Coptidis with BioReF and a good demonstration of using BioReF to uncover the mechanisms of herbs at a systematic level.

Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information

Breast cancer (BC) is one of the most common malignancies that could threaten female health. As the molecular mechanism of BC has not yet been completely discovered, identification of related genes of this disease is an important area of research that could provide new insights into gene function as well as potential treatment targets. Here we used subnetwork extraction algorithms to identify novel BC related genes based on the known BC genes (seed genes), gene co-expression profiles and protein-protein interaction network. We computationally predicted seven key genes (EPHX2, GHRH, PPYR1, ALPP, KNG1, GSK3A and TRIT1) as putative genes of BC. Further analysis shows that six of these have been reported as breast cancer associated genes, and one (PPYR1) as cancer associated gene. Lastly, we developed an expression signature using these seven key genes which significantly stratified 1660 BC patients according to relapse free survival (hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.46–0.65; Logrank p = 5.5e−13). The 7-genes signature could be established as a useful predictor of disease prognosis in BC patients. Overall, the identified seven genes might be useful prognostic and predictive molecular markers to predict the clinical outcome of BC patients.

Epiberberine, a natural protoberberine alkaloid, inhibits urease of Helicobacter pylori and jack bean: Susceptibility and mechanism

In our previous study, Rhizoma Coptidis extract was found to exert more potent inhibitory effect than its major component berberine towards urease from Helicobacter pylori (HPU) and jack bean (JBU). In continuation of our work, the present study was designed to further comparatively investigate the urease inhibitory activities of five major protoberberine alkaloids in Rhizoma Coptidis, namely berberine, palmatine, coptisine, epiberberine, jateorhizine to identify the bioactive constituent, and illuminate the potential mechanism of action. Results indicated that the five protoberberine alkaloids acted as concentration-dependent inactivators of urease with IC₅₀ values ranging between 3.0 and 5087μM for HPU and 2.3->10,000μM for JBU, respectively. Notably, epiberberine (EB) was found to be the most potent inhibitor against both ureases with IC₅₀ values of 3.0±0.01μM for HPU and 2.3±0.01μM for JBU, which was more effective than the standard urease inhibitor, acetohydroxamic acid (83±0.01μM for HPU and 22±0.01μM for JBU, respectively). Further kinetic analysis revealed that the type of EB inhibition against HPU was slow-binding and uncompetitive, with K_i of 10.6±0.01μM, while slow-binding and competitive against JBU with K_i of 4.6±0.01μM. Addition of thiol reagents, such as l-cysteine, glutathione and dithiothreitol, significantly abolished the inhibition, while Ni²⁺ competitive inhibitors, boric acid and sodium fluoride, synergetically inhibited urease with EB, indicating the obligatory role of the active site sulfhydryl group for the inhibition. In addition, binding of EB with the urease proved to be reversible, as about 65% and 90% enzymatic activity of HPU and JBU, respectively, could be restored by dithiothreitol application. These findings highlighted the potential role of Rhizoma Coptidis protoberberine alkaloids, especially EB, as a lead urease inhibitor in the treatment of diseases associated with ureolytic bacteria. Thus, EB had good potential for further development into a promising therapeutic approach for the treatment of urease-related diseases.

DNA Microarray-Based Screening and Characterization of Traditional Chinese Medicine

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.

Screening for the bioactive constituents of traditional Chinese medicines—progress and challenges

The search for lead compounds from traditional Chinese medicines (TCMs) may be promising for new drug development.

Constipation and herbal medicine

Constipation is characterized by a variety of bowel symptoms such as difficulty passing stool, hard stool, and a feeling of incomplete evacuation. The multifactorial causes of constipation limit the clinical efficacy of current conventional treatments that use a single drug that acts through only one pathway. To complement the shortcomings of the current Western medical model and provide a complete holistic approach, herbal medicines capable of targeting multiple organs and cellular sites may be used. In Japan, many herbs and herbal combinations have traditionally been used as foods and medicines. Currently, Japanese physicians use standardized herbal combinations that provide consistent and essential quality and quantity. This review highlights representative Japanese herbal medicines (JHMs), Rhei rhizoma-based JHMs including Daiokanzoto and Mashiningan, and Kenchuto-based JHMs including Keishikashakuyakuto and Daikenchuto, which coordinate the motility of the alimentary tract. This review provides a framework to better understand the clinical and pharmacological efficacies of JHMs on constipation according to the unique theory of Japanese traditional medicine, known as Kampo medicine.

Boldine, a natural aporphine alkaloid, inhibits telomerase at non-toxic concentrations

In a preliminary screening study of natural alkaloids, boldine, an aporphine alkaloid, showed an interesting dose and time dependent anti-proliferative effect in several cancer cell lines. Cytotoxicity of boldine in human fibroblasts was considerably lower than the telomerase positive embryonic kidney HEK293 and breast cancer MCF-7 and MDA-MB-231 cells. Whether boldine can inhibit telomerase was investigated here using a modified quantitative real-time telomere repeat amplification protocol (q-TRAP). This test showed that boldine inhibits telomerase in cells treated with sub-cytotoxic concentrations. Telomerase inhibition occurs via down-regulation of hTERT, the catalytic subunit of the enzyme. Boldine changed the splicing variants of hTERT towards shorter non-functional transcripts as well. A direct interaction of boldine with the enzyme may also be involved, though thermal FRET method did not detect any substantial interaction between boldine and synthetic telomere sequences. This study advocates boldine as a valuable candidate for telomerase-targeted cancer care. This study suggests that derivatives of boldine could be potent anti-cancer drugs.

Systems biology of meridians, acupoints, and chinese herbs in disease

Meridians, acupoints, and Chinese herbs are important components of traditional Chinese medicine (TCM). They have been used for disease treatment and prevention and as alternative and complementary therapies. Systems biology integrates omics data, such as transcriptional, proteomic, and metabolomics data, in order to obtain a more global and complete picture of biological activity. To further understand the existence and functions of the three components above, we reviewed relevant research in the systems biology literature and found many recent studies that indicate the value of acupuncture and Chinese herbs. Acupuncture is useful in pain moderation and relieves various symptoms arising from acute spinal cord injury and acute ischemic stroke. Moreover, Chinese herbal extracts have been linked to wound repair, the alleviation of postmenopausal osteoporosis severity, and anti-tumor effects, among others. Different acupoints, variations in treatment duration, and herbal extracts can be used to alleviate various symptoms and conditions and to regulate biological pathways by altering gene and protein expression. Our paper demonstrates how systems biology has helped to establish a platform for investigating the efficacy of TCM in treating different diseases and improving treatment strategies.

F-actin reorganization and inactivation of rho signaling pathway involved in the inhibitory effect of Coptidis Rhizoma on hepatoma cell migration

HYPOTHESIS

Hepatocellular carcinoma (HCC) is one of the most malignant human tumors and one of the risk factors is its highly metastatic property. Coptidis Rhizoma aqueous extract (CRAE) is able to suppress the migration and invasion of HCC cells, MHCC97-L, and F-actin reorganization and Rho signaling inhibition is involved.

MAIN METHODS

CRAE was prepared and analyzed by high-performance liquid chromatography combined with mass spectrometry. The cytotoxicity and antimigration action of CRAE on MHCC97-L cells were evaluated; Immunofluorescence and immunoblotting were used to investigate the proposed mechanism of CRAE action.

KEY FINDINGS

Chemical analysis reveals that the active components in CRAE are berberine and berberine-like alkaloids. CRAE exhibits a significant inhibitory effect on MHCC97-L cell migration as indicated by wound-healing and invasion-chamber assays. No significant alteration of matrix metalloproteinases and urokinase-type plasminogen activator (uPA) expression were observed in MHCC97-L cells exposed to CRAE. Reduction of F-actin polymerization and damage to cytoskeleton network in MHCC97-L cells were observed after CRAE treatment. Furthermore, it was found that CRAE significantly downregulated the Rho/ROCK signaling pathway.

SIGNIFICANCE

These results indicate that CRAE may act as a Rho/ROCK signaling inhibitor to suppress MHCC97-L cell migration in vitro and suggested that total alkaloids in Coptidis Rhizoma may be a potential agent for suppressing liver cancer invasion.

A new isoquinolinium derivative, Cadein1, preferentially induces apoptosis in p53-defective cancer cells with functional mismatch repair via a p38-dependent pathway

We screened a protoberberine backbone derivative library for compounds with anti-proliferative effects on p53-defective cancer cells. A compound identified from this small molecule library, cadein1 (cancer-selective death inducer 1), an isoquinolinium derivative, effectively leads to a G(2)/M delay and caspase-dependent apoptosis in various carcinoma cells with non- functional p53. The ability of cadein1 to induce apoptosis in p53-defective colon cancer cells was tightly linked to the presence of a functional DNA mismatch repair (MMR) system, which is an important determinant in chemosensitivity. Cadein1 was very effective in MMR(+)/p53(-) cells, whereas it was not effective in p53(+) cells regardless of the MMR status. Consistently, when the function of MMR was blocked with short hairpin RNA in SW620 (MMR(+)/p53(-)) cells, cadein1 was no longer effective in inducing apoptosis. Besides, the inhibition of p53 increased the pro-apoptotic effect of cadein1 in HEK293 (MMR(+)/p53(+)) cells, whereas it did not affect the response to cadein1 in RKO (MMR(-)/p53(+)) cells. The apoptotic effects of cadein1 depended on the activation of p38 but not on the activation of Chk2 or other stress-activated kinases in p53-defective cells. Taken together, our results show that cadein1 may have a potential to be an anti-cancer chemotherapeutic agent that is preferentially effective on p53-mutant colon cancer cells with functional MMR.

Protosappanin A induces immunosuppression of rats heart transplantation targeting T cells in grafts via NF-kappaB pathway

Protosappanin A as one major and effective ingredient from Caesalpinia sappan L. exhibited antirejection activity obviously in heart-transplanted rat. The present study was designed to screen out the potential target genes of protosappanin A with microarray technology and reveal some molecular mechanism of immunosuppressive effect. Rats performed with ectopic peritoneal heart transplantation were randomized into three groups receiving different treatments for 7 days: protosappanin A group (25 mg kg(-1)), cyclosporine A group (10 mg kg(-1)), and control group. The differentially expressed genes responding to protosappanin A were analyzed with microarrays. Among common differentially expressed genes, the ones of interest were selected for further evaluation by real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), Western blot, immunochemistry, immunofluorescence, and ELISA. Among the 146 common differentially expressed genes, NF-kappaB and related genes like IkappaBa, IFN-r, and IP10 were selected for verification. The results of qRT-PCR, Western blot, immunochemistry, and ELISA showed that protosappanin A significantly reduced the expression of NF-kappaB, IFN-r, and IP10 (p < 0.05) and increased IkappaBa expression (p < 0.05) in graft. Moreover, the immunochemistry staining of NF-kappaB and IkappaBa was mainly observed in infiltrating mononuclear cells. Strikingly, immunofluorescent staining localized NF-kappaB to the TCR-positive T cells in graft. Furthermore, protosappanin A exhibited inhibitory effect on T cell proliferation in recipients after 7-day treatment. In conclusion, protosappanin A might act on T cells through inhibiting NF-kappaB activation and downstream gene expressions of IFN-r and IP10, meanwhile reducing T cell proliferation responding to alloantigen, so as to induce immunosuppressive effect. The results encourage a potential therapeutic evaluation of protosappanin A for clinical organ transplantation or other T cell-mediated immune disorders. Additionally, our study also verified the feasibility of microarray utilization in Chinese herb research to explore molecular mechanism and promote development of scientific theories.

Berberine and Coptidis rhizoma as novel antineoplastic agents: a review of traditional use and biomedical investigations

ETHNOPHARMACOLOGICAL RELEVANCE

Coptidis rhizoma (huanglian) and its major component, berberine, have drawn extensive attention toward their antineoplastic effects in the recent years. The antineoplastic effects are related to the Chinese Medicine (CM) properties of huanglian in treating diseases by removing damp-heat and purging fire and counteracting toxicity.

AIM OF THE REVIEW

To trace the long history of the traditional use of huanglian from folk medicines, especially from Chinese medicine, to recent pharmacological studies of huanglian and berberine, with an emphasis on their antineoplastic effects and the promise as novel antineoplastic agents.

METHODS

A total of seven databases were extensively searched for literature research. The terms and keywords for searching included huanglian, berberine, Coptis, Coptidis rhizoma, anticancer, anti-invasion, antimatastasis and mechanism. The papers including ours with studies on anticancer and mechanism, pharmacology and toxicology of huanglian and/or berberine were focused.

RESULTS

In view of traditional use, the anticancer effects of huanglian can be ascribed to its CM trait by removing damp-heat, fire and toxicity. From modern biomedical studies, anticancer effects have been demonstrated in both huanglian and berberine. The underlying molecular mechanisms involve cell-cycle arrest, apoptosis induction and anti-inflammation. Berberine is an essential anticancer compound in huanglian. In some studies, the use of huanglian was shown to be more effective and beneficial than the use of berberine alone. The presence of other protoberberine-type alkaloids in huanglian might give synergistic effects for the anticancer effects. Berberine also demonstrates effects of antiangiogenesis, anti-invasion and anti-metastasis in some cancer cell lines, however, more investigations are required to unravel the underlying mechanisms involved.

CONCLUSIONS

The modern evidences of treating cancer with huanglian and berberine have a strong linkage with traditional concept and rules of using huanglian in CM practice. As anticancer candidates with low toxicity, berberine and its altered structure, as well as huanglian and its formulae, will attract scientists to pursue the potential anticancer effects and the mechanisms by using technologies of genomics, proteomics and other advanced approaches. On the other hand, relatively few in vivo studies have been conducted on anticancer effects of huanglian and berberine. The clinical application of berberine or huanglian as novel cancer therapeutic agents requires in vivo validations and further investigations of their anticancer mechanisms.

Relaxant action mechanism of berberine identified as the active principle of Argemone ochroleuca Sweet in guinea-pig tracheal smooth muscle

In this study we investigated the relaxant effect of the aerial parts of Argemone ochroleuca (Papaveraceae), which is used in Mexican traditional medicine for the treatment of various respiratory diseases such as cough, bronchitis and asthma. The alkaloid berberine was identified as one of the active relaxant principles (EC50 = 118.50 +/-3.91 microM) in the dichloromethane extract of A. ochroleuca (EC50 = 78.03 +/- 2.15 microg mL(-1) with 95.12 +/- 3.56% of relaxation). Berberine concentration-dependently relaxed the carbachol-induced precontractions but not histamine- or KCl-induced precontraction. The relaxant effect of berberine was unaffected by the presence of propranolol (3 microM), glibenclamide (10 microM) or ODQ (10microM). However, 2', 5'-dideoxyadenosine (10 microM) blocked the log concentration-response curves of berberine. On the other hand, berberine produced a leftward shift of the log concentration-response curves of isoproterenol, forskolin and nitroprusside. Additionally, berberine produced a parallel rightward shift of the concentration-response curve of carbachol in a competitive manner with a pA2 of 3.87 +/- 0.045. The above results suggest that the relaxant effect of berberine on tracheal muscle is due to its antagonistic effect on muscarinic acetylcholine receptors.

A polyacetylene compound from herbal medicine regulates genes associated with thrombosis in endothelial cells

From Toki-shakuyaku-san, an herbal formulation for 'cleansing stagnated blood,' a key gene regulatory compound was purified and identified through a screening based on DNA microarray and real-time PCR.

Ethnoveterinary medicines used for ruminants in British Columbia, Canada

BACKGROUND

The use of medicinal plants is an option for livestock farmers who are not allowed to use allopathic drugs under certified organic programs or cannot afford to use allopathic drugs for minor health problems of livestock.

METHODS

In 2003 we conducted semi-structured interviews with 60 participants obtained using a purposive sample. Medicinal plants are used to treat a range of conditions. A draft manual prepared from the data was then evaluated by participants at a participatory workshop.

RESULTS

There are 128 plants used for ruminant health and diets, representing several plant families. The following plants are used for abscesses: Berberis aquifolium/Mahonia aquifolium Echinacea purpurea, Symphytum officinale, Bovista pila, Bovista plumbea, Achillea millefolium and Usnea longissima. Curcuma longa L., Salix scouleriana and Salix lucida are used for caprine arthritis and caprine arthritis encephalitis. Euphrasia officinalis and Matricaria chamomilla are used for eye problems. Wounds and injuries are treated with Bovista spp., Usnea longissima, Calendula officinalis, Arnica sp., Malva sp., Prunella vulgaris, Echinacea purpurea, Berberis aquifolium/Mahonia aquifolium, Achillea millefolium, Capsella bursa-pastoris, Hypericum perforatum, Lavandula officinalis, Symphytum officinale and Curcuma longa. Syzygium aromaticum and Pseudotsuga menziesii are used for coccidiosis. The following plants are used for diarrhea and scours: Plantago major, Calendula officinalis, Urtica dioica, Symphytum officinale, Pinus ponderosa, Potentilla pacifica, Althaea officinalis, Anethum graveolens, Salix alba and Ulmus fulva. Mastitis is treated with Achillea millefolium, Arctium lappa, Salix alba, Teucrium scorodonia and Galium aparine. Anethum graveolens and Rubus sp., are given for increased milk production. Taraxacum officinale, Zea mays, and Symphytum officinale are used for udder edema. Ketosis is treated with Gaultheria shallon, Vaccinium sp., and Symphytum officinale. Hedera helix and Alchemilla vulgaris are fed for retained placenta.

CONCLUSION

Some of the plants showing high levels of validity were Hedera helix for retained placenta and Euphrasia officinalis for eye problems. Plants with high validity for wounds and injuries included Hypericum perforatum, Malva parviflora and Prunella vulgaris. Treatments with high validity against endoparasites included those with Juniperus communis and Pinus ponderosa. Anxiety and pain are well treated with Melissa officinalis and Nepeta caesarea.

The application of DNA micro-arrays (gene arrays) to the study of herbal medicines

DNA micro-arrays (gene arrays) have become a popular and useful tool with which to study the effects of various agents and treatments on gene expression in cells and tissues. In theory one can simultaneously evaluate, in a single experiment, changes in gene expression (at the level of transcription) of the entire genome of the organism under study. Consequently these techniques have been used by many investigators interested in cancer research, differentiation and development, toxicology, and the effects of pharmaceuticals on cells and animals. In addition, recent studies have shown the capacity of the technique for revealing the importance of genes not previously implicated in a given response. However, relatively few attempts have been made so far to evaluate herbal medicines, although the potential to answer a number of relevant questions is there. In this review we first discuss the fundamental principles of the gene array technology, focusing on the individual steps in the process and their problems and pitfalls, and we discuss the analysis and interpretation of the data, the discipline of bio-informatics, without which meaningful evaluation of gene expression changes would be impossible. We next analyze specific studies, which utilized gene array technology, aimed at evaluating the effects of certain herbal medicine formulas and bioactive ingredients in animal tissues and in cell cultures. We also include a brief description of our own evaluation of Echinacea, which we have been studying for several years, to indicate possible mechanisms of action of this herbal, and also to illustrate how the techniques, especially the bio-informatics, continue to evolve. We believe, on the basis of experience acquired by us and other investigators to date, that the technology of gene array analysis can make significant contributions to understanding how herbal medicines work, and therefore can validate their applications in medicine.

DNA microarrays in herbal drug research

Natural products are gaining increased applications in drug discovery and development. Being chemically diverse they are able to modulate several targets simultaneously in a complex system. Analysis of gene expression becomes necessary for better understanding of molecular mechanisms. Conventional strategies for expression profiling are optimized for single gene analysis. DNA microarrays serve as suitable high throughput tool for simultaneous analysis of multiple genes. Major practical applicability of DNA microarrays remains in DNA mutation and polymorphism analysis. This review highlights applications of DNA microarrays in pharmacodynamics, pharmacogenomics, toxicogenomics and quality control of herbal drugs and extracts.

Effect of berberine on proliferation, biosynthesis of macromolecules, cell cycle and induction of intercalation with DNA, dsDNA damage and apoptosis in Ehrlich ascites carcinoma cells

Our primary aim was to study berberine, a potential anti-cancer drug, for its cytotoxic and antiproliferative activity in-vitro using Ehrlich ascites carcinoma (EAC) cells. Cytotoxicity was measured by the growth inhibition assay. We investigated the effect of berberine on the biosynthesis of macro-molecules (DNA, RNA, proteins), cell cycle effects and induction of dsDNA damage and apoptosis in berberine-treated EAC cells. Our results showed that berberine acts cytotoxically on EAC cells. The cytotoxicity was directly concentration and time dependent. The highest cytotoxic concentrations (100 and 50 microg mL(-1)) induced intercalation of berberine with DNA, formation of dsDNA breaks, inhibition of DNA synthesis and death of EAC cells. A concentration of 10 mug mL(-1) induced clear apoptotic cell death, which was followed by inhibition of protein synthesis.

Involvement of c-myc-regulated genes in hepatocellular carcinoma related to genotype-C hepatitis B virus

PURPOSE

The purpose of this study was to elucidate the molecular basis of hepatocellular carcinoma (HCC) caused by genotype-C hepatitis B virus (HBV).

METHODS

We compared molecular profiles of 15 HCCs and five non-tumorous livers, all of which were associated with genotype-C HBV infection, using DNA microarray technology.

RESULTS

Our supervised learning identified 237 genes whose expression differed between HCCs and non-tumorous livers. This result was validated by a false discovery rate of 0%. Levels of expression of 35 and 202 genes were higher and lower, respectively, in HCCs than in non-tumorous livers. Among the 237 genes, we highlighted the top 35 upregulated and top 35 down regulated genes in tumor. Interestingly, when overlapping genes were excluded, 12 (e.g., NM23-H2, MCM7, PARP1, YWHAH, HSPB1, and MSH2) of the top 34 upregulated genes and five (e.g., MT1A and MT3) of the top 33 downregulated genes were c-myc-regulated genes. The microarray data for five randomly selected genes (MCM7, UBE2L3, PPIA, CXCL12, and ASS) were confirmed by quantitative real-time reverse transcription-polymerase chain reaction.

CONCLUSIONS

Our results indicate that many c-myc-regulated genes are involved in genotype-C-HBV-related HCC, suggesting that c-myc is related to the hepatocarcinogenic activity of genotype-C HBV.

Micellar electrokinetic chromatography for separation of a mixture of coptis alkaloids, scute flavonoids, and rhubarb anthraquinones and bianthrones

Coptidis Rhizoma, Scutellariae Radix, and Rhei Rhizoma are three common Chinese herbs. There are many herbal formulas which contain either two or all three of the herbs mentioned above. Their bioactive components have already been identified, respectively. However, there is no report about separation of the 13 bioactive constituents of the three herbs at the same time. In order to assess these constituents of related Chinese herbal preparations, a micellar electrokinetic chromatography method was developed. While buffer pH and surfactant concentration affected the resolution of separation, acetonitrile percentage was found to significantly influence the resolution, peak shape, and elution window. Optimum separation of 13 compounds was achieved at pH 7.3 using a buffer mixture of 70% (v/v) 3 mM di-sodium tetraborate, 10 mM sodium dihydrogen phosphate, and 50 mM sodium deoxycholate with 30% (v/v) acetonitrile. When applying the developed method to analyze a model preparation, San-huang-xie-xin-tang, which contains all three herbs, 8 of the 13 bioactive constituents, could be determined. The present study proposed a method to assess San-huang-xie-xin-tang within short analysis time and also provided a possible starting point to evaluate related herbal preparations containing Coptidis Rhizoma, Scutellariae Radix, and Rhei Rhizoma.

Investigation of differentially expressed proteins due to the inhibitory effects of berberine in human liver cancer cell line HepG2

The investigation of differentially expressed proteins was used together with other techniques to study the inhibitory effects of two different doses of berberine in human liver cancer cell line HepG2. For HepG2 cells treated with 24.0 mg l(-1) of berberine, an increase in the sub G(0) phase that was indicative of cell death was observed in cell cycle analysis with flow cytometry. However, no significant increase in sub G(0) was observed in HepG2 cells treated with 4.0 mg l(-1) of berberine. Using flow cytometric analysis, significant activation of caspase 3 was not observed with HepG2 cells treated with 4.0 and 24.0 mg l(-1) of berberine. In this work, labeling of cells with stable isotope was not used in the proposed method developed. The whole cell lysates from the control and treated cells were digested with trypsin and the peptides were separated by two-dimensional (cation exchange and reversed phase) liquid chromatography and tandem mass spectrometry. Our preliminary data showed that the proposed platform provided a rapid approach to study the molecular mechanism due to the inhibitory effects of different doses of the berberine on HepG2 cell lines. This included a network of proteins involved in mitogen-activated protein kinase (MAPK) phosphorelay systems, metabolism, regulation of cell cycle and DNA damage response. The differentially expressed proteins identified using the current approach were consistent with the data obtained from cell cycle analysis with flow cytometry.

Berberine-antiproliferative activity in vitro and induction of apoptosis/necrosis of the U937 and B16 cells

Berberine, an isoquinoline plant alkaloid, is widely distributed in plants used in the traditional Chinese medicine. It displays a wide range of biological activities and the mechanism of action. Our previous studies of the anticancer activity of berberine against the cancer cell lines HeLa and L1210 were extended to the human tumour U937 cell line and the murine melanoma B16 cell line growing in vitro. Cytotoxicity was measured by the growth inhibition assay and by the cell morphology monitoring. The in vitro cytotoxic studies were complemented by the cell cycle analysis and determination of apoptotic DNA fragmentation. Berberine acted cytotoxically on both tumour cell lines. The melanoma B16 cells were much more sensitive to berberine treatment than the U937 cells. The value of IC(100) was below 100 microg/ml for the U937 cells and below 1 microg/ml for the B16 cells. As for both cell lines under the long-term influence the values of IC(50) were found to be less than 4 microg/ml. No effect of berberine on the cell cycle profile of the U937 and B16 cells was detected, however, berberine induced apoptosis of the U937 cells. On the other hand, cell lysis/necrosis of the berberine-treated B16 cells was observed as the result of the integrity damage of the cytoplasmic membrane.

The extract of huanglian, a medicinal herb, induces cell growth arrest and apoptosis by upregulation of interferon-beta and TNF-alpha in human breast cancer cells

Huanglian (Coptidis rhizoma), a widely used herb in traditional Chinese medicine, has been shown recently to possess anticancer activities. However, the molecular mechanism underlying the anticancer effect of the herb is poorly understood. Specifically, whether huanglian extract affects the expression of cancer-related genes has not been defined. This study used DNA microarray technology to examine the effect of the herbal extract on expression of the common genes involved in carcinogenesis in two human breast cancer cell lines, the ER-positive MCF-7 and ER-negative MDA-MB-231 cells. Treatment of the cancer cells with huanglian extract markedly inhibited their proliferation in a dose- and time-dependent manner. The growth inhibitory effect was much more profound in MCF-7 cell line than that in MDA-MB-231 cells. DNA microarray assay revealed that treatment with huanglian dramatically increased the mRNA expression of interferon-beta (IFN-beta) and tumor necrosis factor-alpha in MCF-7 cells. Quantitative analysis by real-time PCR or western blotting confirmed the upregulation of the two genes (especially IFN-beta) in MCF-7 cells, but not in MDA-MB-231 cells. Addition of neutralizing antibody against IFN-beta to culture medium markedly inhibited the huanglian-induced antiproliferative effect, confirming the involvement of IFN-beta in the huanglian's effect and also suggesting an autocrine pathway for the action of IFN-beta in this setting. Given that IFN-beta is among the most important anticancer cytokines, the upregulation of this gene by huanglian is, at least in part, responsible for its antiproliferative effect. The results of this study implicate huanglian as a promising herb for chemoprevention and chemotherapy of certain cancers.

Molecular dissection of a medicinal herb with anti-tumor activity by oligonucleotide microarray

It is difficult to understand precisely the physiological actions of herbs because they contain a complex array of constituent molecules. In the present study we used DNA microarray data for 12600 genes to examine the anti-proliferative activity of the herb Coptidis rhizoma and eight constituent molecules against eight human pancreatic cancer cell lines. We identified 27 genes showing strong correlation with the 50% inhibitory dose (ID50) of C. rhizoma after 72-h exposure. Hierarchical cluster analysis with correlation coefficients between expression levels of these 27 C. rhizoma-related genes and the ID50 of each constituent molecule classified these test molecules into two clusters, one consisting of C. rhizoma and berberine and the other consisting of the remaining seven molecules. Our results suggest that one molecule, berberine, can account for the majority of the anti-proliferative activity of C. rhizoma and that DNA microarray analyses can be used to improve our understanding of the actions of an intact herb.

Self-organizing-map-based molecular signature representing the development of hepatocellular carcinoma

Using high-density oligonucleotide array, we comprehensively analyzed expression levels of 12600 genes in 50 hepatocellular carcinoma (HCC) samples with positive hepatitis C virus (HCV) serology (well (G1), moderately (G2), and poorly (G3) differentiated tumors) and 11 non-tumorous livers (L1 and L0) with and without HCV infection. We searched for discriminatory genes of transition (L0 vs. L1, L1 vs. G1, G1 vs. G2, G2 vs. G3) with a supervised learning method, and then arranged the samples by self-organizing map (SOM) with the discriminatory gene sets. The SOM arranged the five clusters on a unique sigmoidal curve in the order L0, L1, G1, G2, and G3. The sample arrangement reproduced development-related features of HCC such as p53 abnormality. Strikingly, G2 tumors without venous invasion were located closer to the G1 cluster, and most G2 tumors with venous invasion were located closer to the G3 cluster (P=0.001 by Fisher's exact test). Our present profiling data will serve as a framework to understand the relation between the development and dedifferentiation of HCC.

Effects of Si-Jun-Zi decoction polysaccharides on cell migration and gene expression in wounded rat intestinal epithelial cells

Si-Jun-Zi decoction (SJZD), a traditional Chinese herbal prescription, has been used clinically for treating patients with disorders of the digestive system. Previous studies indicated that the polysaccharides of SJZD (SJZPS) are the active components contributing towards its pharmacological effects in improving gastrointestinal function and immunity. However, the protective and restitutive effects on intestinal epithelial cells remain unknown. In the present study, SJZPS were first extracted and chemically characterized. Then their stimulatory and restitutive effects on intestinal epithelial cells (IEC-6 cells) were elicited by different in vitro models including migration of wounded IEC-6 cells and cell proliferation. Results indicated that SJZPS not only protects the cells against the harmful impairment of indomethacin but also enhances re-epithelialization of a wounded monolayer at an optimal dose of 100 mug/ml at 24 h incubation. To elucidate the modulatory effect of SJZPS on wounded IEC-6 cells at the molecular level, an oligonucleotide microarray was employed to study differential gene expression of SJZPS-treated IEC-6 cells and the candidate genes were validated by RT-PCR. There was increased expression of genes coding for ion channels and transporters, which are critical to cell migration and restoration of wounded intestinal cells, suggesting a possible mechanism for re-epithelialization. In conclusion, our data show for the first time that SJZPS can enhance intestinal restitution and protect against indomethacin-induced damage of intestinal epithelial cells. These findings provide new insight into the mechanism of action of a traditional Chinese herbal prescription, SJZD, in intestinal wound restitution.

Potential anticancer activity of tanshinone IIA against human breast cancer

Tanshinone IIA is a derivative of phenanthrene-quinone isolated from Danshen, a widely used Chinese herbal medicine. It has antioxidant properties and cytotoxic activity against multiple human cancer cell lines, inducing apoptosis and differentiation of some human cancer cell lines. Our purpose was to confirm its anticancer activity on human breast cancer in vitro and in vivo and to elucidate the mechanism of its activity. Human breast cancer cells were tested in vitro for cytotoxicity, colony formation inhibition, BrdU incorporation and gene expression profiling after treatment with tanshinone IIA. Seven nude mice bearing human breast infiltrating duct carcinoma orthotopically were tested for anticancer activity and expression of caspase-3 in vivo by s.c. injection of tanshinone IIA at a dose of 30 mg/kg 3 times/week for 10 weeks. Tanshinone IIA demonstrated a dose- and time-dependent inhibitory effect on cell growth (IC50 = 0.25 microg/ml), and it significantly inhibited colony formation and BrdU incorporation of human breast cancer cells. Oligonucleotide microarray analysis identified 41 upregulated (1.22%) and 24 downregulated (0.71%) genes after tanshinone IIA treatment. Upregulated genes were involved predominantly in cycle regulation, cell proliferation, apoptosis, signal transduction and transcriptional regulation; and downregulated genes were associated mainly with apoptosis and extracellular matrix/adhesion molecules. A 44.91% tumor mass volume reduction and significant increase of casepase-3 protein expression were observed in vivo. Our findings suggest that tanshinone IIA might have potential anticancer activity on both ER-positive and -negative breast cancers, which could be attributed in part to its inhibition of proliferation and apoptosis induction of cancer cells through upregulation and downregulation of multiple genes involved in cell cycle regulation, cell proliferation, apoptosis, signal transduction, transcriptional regulation, angiogenesis, invasive potential and metastatic potential of cancer cells. ADPRTL1 might be the main target at which tanshinone IIA acted.

Molecular signature linked to acquired resistance to cisplatin in esophageal cancer cells

To clarify the molecular basis of acquired cisplatin (CDDP) resistance in esophageal squamous cell carcinoma (ESCC), we used cDNA microarray technology. A CDDP-resistant cell line (YES-2/CDDP), which shows a 7.5-fold increase in resistance to CDDP and a 3-fold decrease in CDDP accumulation compared with the parental YES-2 ESCC cell line, was generated from YES-2 by exposure to increased concentrations of CDDP. By cDNA microarray analysis, we identified 44 genes with significantly different expression levels between YES-2/CDDP and YES-2 cells. Interestingly, 15 of these 44 genes encoded ribosome-related proteins, almost all of which were underexpressed in YES-2/CDDP cells. Our present data suggest that many ribosome-related genes may be involved in the acquired resistance to CDDP in ESCC and that such information may allow us to better understand the mechanism of CDDP resistance.