Shih-Lan Hsu

Selection of DDX5 as a novel internal control for Q-RT-PCR from microarray data using a block bootstrap re-sampling scheme

BackgroundThe development of microarrays permits us to monitor transcriptomes on a genome-wide scale. To validate microarray measurements, quantitative-real time-reverse transcription PCR (Q-RT-PCR) is one of the most robust and commonly used approaches. The new challenge in gene quantification analysis is how to explicitly incorporate statistical estimation in such studies. In the realm of statistical analysis, the various available methods of the probe level normalization for microarray analysis may result in distinctly different target selections and variation in the scores for the correlation between microarray and Q-RT-PCR. Moreover, it remains a major challenge to identify a proper internal control for Q-RT-PCR when confirming microarray measurements.ResultsSixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. By this approach, we identified DDX5 as a novel internal control for Q-RT-PCR. Twenty-three genes, which were differentially expressed between adjacent normal and tumor samples, were selected and analyzed using 24 paired lung adenocarcinoma samples by Q-RT-PCR using two internal controls, DDX5 and GAPDH. The percentage correlation between Q-RT-PCR and microarray were 70% and 48% by using DDX5 and GAPDH as internal controls, respectively.ConclusionTogether, these quantification strategies for Q-RT-PCR data processing procedure, which focused on minimal variation, ought to significantly facilitate internal control evaluation and selection for Q-RT-PCR when corroborating microarray data.

Norcantharidin‐induced apoptosis is via the extracellular signal‐regulated kinase and c‐Jun‐NH2‐terminal kinase signaling pathways in human hepatoma HepG2 cells

Norcantharidin (NCTD) is an anticancer drug routinely used against hepatoma in China. Previously, we reported that NCTD could induce mitotic arrest and apoptosis in human hepatoma HepG2 cells. However, the intracellular signaling pathways involved in NCTD‐induced apoptotic cell death are still obscure. Caspase inhibitors were used to clarify the role of specific caspase in NCTD‐triggered apoptotic process. Results showed that activation of caspase‐9/caspase‐3 cascade is required for NCTD‐induced apoptotic death. To decipher the upstream signals for NCTD‐induced apoptosis, we characterized the involvement of mitogen‐activated protein kinases (MAPKs), including extracellular signal‐regulated kinase (ERK), c‐Jun NH2‐terminal kinase (JNK), and p38MAPK. The role of their downstream targets, transcription factors activating protein‐1 (AP‐1), and nuclear factor κB (NF‐κB) in NCTD‐induced apoptosis was also analyzed. Immunoblot analyses and in vitro kinase assay demonstrated that NCTD‐induced apoptosis was accompanied by the elevations of the levels of phosphorylated form and kinase activity of ERK and JNK, but not p38MAPK. The inhibitor of ERK pathway (U0126 or PD98059) or JNK pathway (SP600125) markedly prevented kinase activation, and also greatly reduced NCTD‐induced apoptotic cell death. Increased DNA‐binding activity of AP‐1 and NF‐κB was also observed after NCTD treatment. Inhibition of NF‐κB activation by PDTC or inhibition of AP‐1 activation by curcumin drastically blocked NCTD‐induced cell death. These results imply that activation of ERK and JNK, and modulation of downstream transcription factors NF‐κB and AP‐1, may be involved in NCTD‐induced apoptosis.

Anti-inflammatory effects of methanol extract of Antrodia cinnamomea mycelia both in vitro and in vivo.

AIMS OF THE STUDY Antrodia cinnamomea is a folk medicinal mushroom commonly used in Taiwan for the treatment of several types of cancers and inflammatory disorders. This study aimed to explore the folk use of Antrodia cinnamomea on pharmacological grounds to characterize the scientific basis of anti-inflammatory activity. MATERIALS AND METHODS The in vitro anti-inflammatory activity of methanol extract of liquid cultured mycelia of Antrodia cinnamomea (MEMAC) was judged by the measurement of the produced levels of pro-inflammatory cytokines and mediators in lipopolysaccharide (LPS)-stimulated RAW264.7 cells and human peripheral blood mononuclear cells (PBMCs). The in vivo anti-inflammatory activity of MEMAC was evaluated using carrageenan-induced hind paw edema in mice, the activities of catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GPx) in the liver and the levels of malondialdehyde (MDA) and nitrite oxide (NO) in the edema paw. The levels of serum NO and TNF-α were measured. The MEMAC was administered at the concentrations of 100, 200, and 400mg/kg body weight of mouse. RESULTS MEMAC inhibited the production of LPS-induced pro-inflammatory cytokines (TNF-α and IL-6) and mediators (NO and PGE2) in RAW264.7 cells and human PBMCs. Data from Western blotting showed that MEMAC decreased the levels of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) protein expression in LPS-stimulated RAW264.7 macrophages. In vivo, MEMAC showed significant (p<0.05) anti-inflammatory activity by reducing the edema volume in carrageenan-induced paw edema in mice. MEMAC (400mg/kg) also reduced the carrageenan-induced leukocyte migration (50.92±5.71%). Further, MEMAC increased the activities of CAT, SOD, and GPx in the liver tissue and decreased the levels of serum NO and TNF-α after carrageenan administration. CONCLUSIONS Our results showed that MEMAC has the anti-inflammatory property both in vitro and in vivo, suggesting that it may be a potential preventive or therapeutic candidate for the treatment of inflammatory disorders.

Methyl antcinate A from Antrodia camphorata induces apoptosis in human liver cancer cells through oxidant-mediated cofilin- and Bax-triggered mitochondrial pathway.

We investigated the effects of antcin A, antcin C, and methyl antcinate A (MAA) isolated from Antrodia camphorata on the proliferation of human liver cancer cell lines Huh7, HepG2, and Hep3B and the normal cell rat hepatocytes. The three compounds selectively inhibit the proliferation of tumor cells rather than normal cells, with IC(50) values ranging from 30.2 to 286.4 microM. The compound MAA was a more potent cytotoxic agent than antcins A and C with IC(50) values of 52.2, 78.0, and 30.2 microM against HepG2, Hep3B, and Huh7 cells, respectively. To elucidate the molecular mechanism, treatment of Huh7 cells with 100 microM MAA induced an apoptotic cell death, which was characterized by the appearance of sub-G1 population, DNA fragmentation, TUNEL positive cells, and caspase activation. MAA triggered the mitochondrial apoptotic pathway, as indicated by an increase in the protein expression of Bax, Bak, and PUMA, as well as a decrease in Bcl-(XL) and Bcl-2 and disruption of mitochondrial membrane potential and promotion of mitochondrial cytochrome c release, as well as activation of caspases-2, -3, and -9. We also found that pretreatment with inhibitors of caspases-2, -3, and -9 noticeably blocked MAA-triggered apoptosis. Furthermore, intracellular reactive oxygen species (ROS) generation and NADPH oxidase activation were observed in MAA-stimulated Huh7 cells. Mechanistic studies showed that MAA induces mitochondrial translocation of cofilin. When Huh7 cells were treated with cyclosporine A and bongkrekic acid, an inhibitor of the mitochondria permeability transition pore, the levels of cell death induced by MAA were significantly attenuated. Additionally, pretreatment of Huh7 cells with antioxidants ascorbic acid and N-acetyl cysteine markedly attenuated the MAA-induced apoptosis by upregulation of Bax, Bak, and PUMA, mitochondrial translocation of cofilin, activation of caspase-3, and cell death. Taken together, our results provide the first evidence of the activation of the ROS-dependent cofilin- and Bax-triggered mitochondrial pathway as a critical mechanism of MAA-induced cell death in liver cancer cells.

Gene expression profiles of the aurora family kinases.

The evolutionarily conserved Aurora family kinases, a family of mitotic serine/threonine kinases, has three members in humans (Aurora-A, -B and -C). Overexpression of Aurora family members, particularly Aurora-A, has been reported in many human cancers and cell lines. In this study, we present evidence based on comparative gene expression analysis via quantitative RT-PCR to delineate the relative contributions of these kinases in 60 cell lines and statistical analysis in five different human cancer microarray datasets. The analysis demonstrated the selective upregulation of these Aurora members in various cancers. In general, Aurora-A exhibited the highest expression levels, with substantially decreased quantities of the Aurora-C transcript detected relative to Aurora-A and -B. Moreover, to characterize the roles of each Aurora member, which share many similarities, we investigated the expression profiles of the family in normal tissues and a panel of different phases of the HeLa cell cycle. Finally, both Aurora-A and -B were overexpressed in a majority of esophageal tumor tissues in comparison to the normal variants. Taken together, the results show that each Aurora member exhibits distinct expression patterns, implying that they are engaged in different biological processes to accomplish more elaborate cell physiological functions in higher organisms.

High transport critical currents and flux jumps in bulk YBa2Cu3Ox superconductors

A preferentially oriented bulk YBa2Cu3Ox superconductor was prepared by the liquid phase method. A continuous dc current carrying capacity exceeding 120 A with current density higher than 37 300 A/cm2 at 77 K has been obtained. The high current effects causing fracture of the sample were studied in relation to the thermal diffusion properties. In magnetization measurements, flux jumps were observed for currents in the sample a‐b plane below the temperature of about 20 K. The jumps are more closely spaced with decreasing temperature or increasing field sweep rates.

Caspase 3, periodically expressed and activated at G2/M transition, is required for nocodazole-induced mitotic checkpoint

Caspases have been known for several years for their involvement in executing apoptosis, where unwanted or damaged cells are eliminated. Surprisingly, after analysis of the relevant data set from the Stanford microarray database, we noticed that the gene expression pattern for caspase 3, but not for caspase 1, 6, 7, 8, 9, or 10, undergoes periodic change in the HeLa cell cycle. In this study, we have demonstrated that caspase 3, but not other caspases, is upregulated and activated just prior to mitosis. Pretreatment of human hepatoma cells with a caspase 3 inhibitor z-DEVD-FMK, prior to the treatment with an antimicrotubule drug nocodazole, abrogates the mitotic arrest, suggesting that caspase 3 (or a caspase 3-like enzyme) might be involved in mitotic-spindle checkpoint. The studies not only characterize caspase 3 as a cell cycle-regulated protein, but also link the protein to nocodazole-dependent mitotic checkpoint, greatly expanding the understanding of caspase 3.

Graptopetalum Paraguayense Ameliorates Chemical-Induced Rat Hepatic Fibrosis In Vivo and Inactivates Stellate Cells and Kupffer Cells In Vitro

Background Graptopetalum paraguayense (GP) is a folk herbal medicine with hepatoprotective effects that is used in Taiwan. The aim of this study was to evaluate the hepatoprotective and antifibrotic effects of GP on experimental hepatic fibrosis in both dimethylnitrosamine (DMN)- and carbon tetrachloride (CCl4)-induced liver injury rats. Methods Hepatic fibrosis-induced rats were fed with the methanolic extract of GP (MGP) by oral administration every day. Immunohistochemistry, biochemical assays, and Western blot analysis were performed. The effects of MGP on the expression of fibrotic markers and cytokines in the primary cultured hepatic stellate cells (HSCs) and Kupffer cells, respectively, were evaluated. Results Oral administration of MGP significantly alleviated DMN- or CCl4-induced liver inflammation and fibrosis. High levels of alanine transaminase, aspartate transaminase, bilirubin, prothrombin activity and mortality rates also decreased in rats treated with MGP. There were significantly decreased hydroxyproline levels in therapeutic rats compared with those of the liver-damaged rats. Collagen I and alpha smooth muscle actin (α-SMA) expression were all reduced by incubation with MGP in primary cultured rat HSCs. Furthermore, MGP induced apoptotic cell death in activated HSCs. MGP also suppressed lipopolysaccharide-stimulated rat Kupffer cell activation by decreasing nitric oxide, tumor necrosis factor-α and interleukin-6 production, and increasing interleukin-10 expression. Conclusions The results show that the administration of MGP attenuated toxin-induced hepatic damage and fibrosis in vivo and inhibited HSC and Kupffer cell activation in vitro, suggesting that MGP might be a promising complementary or alternative therapeutic agent for liver inflammation and fibrosis.

The possible origin of power-law magnetic relaxation in high-Tc superconductors

Abstract The power-law magnetic relaxation of high-Tc superconductors can be derived from the flux-creep equation by using the logarithmic-current dependence of the effective pinning energy. The exponent β and relaxation rate R of power law are represented by elementary parameters; activation barrier γ, current density J0, attempt velocity V0, and grain dimension d. The validity of this theory is confirmed by experiments on a melt-textured YBa2Cu3O7−δ sample. Using this theory, average pinning energy as functions of temperature, applied field, and process of this sample has been calculated and discussed.

Destruxin B Isolated from Entomopathogenic Fungus Metarhizium anisopliae Induces Apoptosis via a Bcl-2 Family-Dependent Mitochondrial Pathway in Human Nonsmall Cell Lung Cancer Cells

Destruxin B, isolated from entomopathogenic fungus Metarhizium anisopliae, is one of the cyclodepsipeptides with insecticidal and anticancer activities. In this study, destruxin B was extracted and purified by ion-exchange chromatography, silica gel chromatography, and semipreparative high-performance liquid chromatography. The potential anticancer effects and molecular mechanisms of destruxin B in human nonsmall cell lung cancer cell lines were characterized. Our results showed that destruxin B induced apoptotic cell death in A549 cells. This event was accompanied by the activation of caspase-2, -3, and -9. Moreover, destruxin B increased the expression level of proapoptotic molecule, PUMA, while decreased antiapoptotic molecule Mcl-1. Additionally, the translocation of Bax from cytosol to mitochondrial membrane was observed upon destruxin B treatment. Knockdown of Bax by shRNA effectively attenuated destruxin-B-triggered apoptosis in A549 cells. Interestingly, similar toxic effects and underlying mechanisms including caspase activation, upregulation of PUMA, and downregulation of Mcl-1 were also observed in a p53-null lung cancer H1299 cell line upon destruxin B treatment. Taken together, our findings suggest that destruxin-B-induced apoptosis in human nonsmall cell lung cancer cells is via a Bcl-2 family-dependent mitochondrial pathway.