Published literature

Safety Assessment (22) Products

  Mouse OneArray  
 Molecular Medicine Reports. 2015, 11(2):887-95. doi: 10.3892/mmr.2014.2823.
 Biological effect of ketamine in urothelial cell lines and global gene expression analysis in the bladders of ketamine‑injected mice 
 CHENG‑HUANG SHEN, SHOU‑TSUNG WANG, YING‑RAY LEE, SHIAU‑YUAN LIU, YI‑ZHEN LI, JIANN‑DER WU, YI‑JU CHEN, Yi‑Wen Liu
  Abstract
Ketamine is used clinically for anesthesia but is also abused as a recreational drug. Previously, it has been established that ketamine‑induced bladder interstitial cystitis is a common syndrome in ketamine‑abusing individuals. As the mechanisms underlying ketamine‑induced cystitis have yet to be revealed, the present study investigated the effect of ketamine on human urothelial cell lines and utilized a ketamine‑injected mouse model to identify ketamine‑induced changes in gene expression in mice bladders. In the in vitro bladder cell line assay, ketamine induced cytotoxicity in a dose‑ and time‑dependent manner. Ketamine arrested the cells in G1 phase and increased the sub‑G1 population, and also increased the barrier permeability of these cell lines. In the ketamine‑injected mouse model, ketamine did not change the body weight and bladder histology of the animals at the dose of 30 mg/kg/day for 60 days. Global gene expression analysis of the animals' bladders following data screening identified ten upregulated genes and 36 downregulated genes induced by ketamine. A total of 52% of keratin family genes were downregulated, particularly keratin 6a, 13 and 14, which was confirmed by polymerase chain reaction analysis. Keratin 14 protein, one of the 36 ketamine‑induced downregulated genes, was also reduced in the ketamine‑treated mouse bladder, as determined by immunohistochemical analysis. This suggested that cytotoxicity and keratin gene downregulation may have a critical role in ketamine‑induced cystitis.
   

  Human OneArray  
 Toxicology Research. 2015, 4, 365-375. doi: 10.1039/C4TX00181H.
 A gene signature for gold nanoparticle-exposed human cell lines
 
 
 Ruei-Yue Liang, Hsin-Fang Tu, Xiaotong Tan, Yu-Shan Yeh, Pin Ju Chueh, Show-Mei Chuang
  Abstract
There is currently a significant need for effective methods aimed at diagnosing and screening for nanoparticle exposure. We previously investigated the toxicity of three different particle sized gold nanoparticles (AuNPs) toward different types of mammalian cells and explored a related gene expression profile by cDNA microarray analysis of AuNP-exposed MRC-5 cells. In this study, we sought to further identify genes that could be used as biomarkers for AuNP exposure. We used cDNA microarray analysis to obtain comprehensive gene expression profiles from A549 cells exposed to three different-sized AuNPs. A total of 409 genes were commonly up-regulated by the tested AuNPs; of them, 71 had previously been analyzed to be up-regulated in MRC-5 cells. Among the top-ranked 30 of these 71 up-regulated genes, based on the magnitude of induction, nine genes were confirmed to be transcriptionally induced in A549 cells by all three tested AuNPs, as assessed by quantitative real-time polymerase chain reaction (qPCR). Among them, TSC22D3, TRIB3, PCK2 and DDIT4 were the most sensitive to the three AuNPs, and showed dose-dependent changes in several human cell lines. qPCR and immunoblotting analyses revealed that the same concentrations of micro-Au and nano-TiO2 failed to elicit up-regulation of these four genes at the mRNA and protein levels in any tested cell lines. Although the definition and practical implementation of specific biomarkers for nanoparticles is still in its infancy, our data suggest that it may be possible to define reliable biomarkers for the diagnosis of nanomaterial exposure.
   

  Mouse&Rat miRNA OneArray  
 Environmental Toxicology. 2015, 30(6):712-23. doi: 10.1002/tox.21949.
 Prenatal and neonatal exposure to perfluorooctane sulfonic acid results in aberrant changes in miRNA expression profile and levels in developing rat livers
 
 
 Fan Wang, Yihe Jin, Faqi Wang, Junsheng Ma, Wei Liu
  Abstract
Perfluorooctane sulfonate (PFOS) is an animal carcinogen. However, the underlying mechanism in cancer initiation is still largely unknown. Recently identified microRNAs (miRNAs) may play an important role in toxicant exposure and in the process of toxicant-induced tumorigenesis. We used PFOS to investigate PFOS-induced changes in miRNA expression in developing rat liver and the potential mechanism of PFOS-induced toxic action. Dams received 3.2 mg/kg PFOS in their feed from gestational day 1 (GD1) to postnatal day 7 (PND 7). Pups then had free access to treated feed until PND 7. We isolated RNAs from liver tissues on PND 1 and 7 and analyzed the expression profiles of 387 known rat miRNAs using microarray technology. PFOS exposure induced significant changes in miRNA expression profiles. Forty-six miRNAs had significant expression alterations on PND 1, nine miRNAs on PND 7. Specifically, expression of four miRNAs was up-regulated on PND 7 but down-regulated on PND1 (p < 0.05). Many aberrantly expressed miRNAs were related to various cancers. We found oncogenic and tumor-suppressing miRNAs, which included miR-19b, miR-21*, miR-17-3p, miR-125a-3p, miR-16, miR-26a, miR-1, miR-200c, and miR-451. In addition, four miRNAs were simultaneous significantly expressed on both PND 1 and 7. Functional Annotation analysis of the predicted transcript targets revealed that PFOS exposure potentially alters pathways associated with different cancers (cancer, melanoma, pancreatic cancer, colorectal cancer, and glioma), biological processes which include positive regulation of apoptosis and cell proliferation. Results showed PFOS exposure altered the expression of a suite of miRNAs.
   

  Rat OneArray  
 Transactions of Tianjin University. 2014, 20: 451-457. doi: 10.1007/s12209-014-2294-7.
 Transcriptomic Analysis of Aflatoxin B1-Regulated Genes in Rat Hepatic Epithelial Cells
 
 
 Liu Yang, Guanghui Li, Junwen Li, Zhaoli Chen, Jing Ji, Haiyong Wang
  Abstract
Aflatoxins are the most popular hepatotoxicants. Chronic exposure to aflatoxins leads to a wide variety of liver diseases, such as hepatocellular carcinoma. In this study, we analyzed the genome wide expression profiles of aflatoxin B1-induced rat hepatic epithelial cells. The expression of 325, 184 and 199 special genes was altered when exposed to 0.03, 0.1 and 0.2 弮mol/L aflatoxin B1 respectively, and 239 genes were commonly expressed. After the functional analysis on these dose-special genes, we determined several key pathways related to hepatotoxicity, such as TGF-beta signaling pathway, tight junction, adherens junction, the regulation of actin cytoskeleton, ErbB signaling pathway, p53 signaling pathway, pathways in cancer and axon guidance. Common genes were mainly associated with focal adhesion, ECM-receptor interaction, and cell adhesion molecules. Gene ontology annotations showed a good concordance with these pathways. The quantitative real-time polymerase chain reaction(PCR) analysis of selected genes showed similar patterns in microarrays. The toxicogenomic study provides a better understanding of molecular mechanisms of aflatoxins.
   

  Mouse&Rat miRNA OneArray  
 Cell Death & Disease. 2014 Oct 2. doi: 10.1038/cddis.2014.407.
 MicroRNA-207 enhances radiation-induced apoptosis by directly targeting Akt3 in cochlea hair cells
 
 
 Y-w Yuan, P-x Tan, S-s Du, C Ren, Q-w Yao, R Zheng, R Li
  Abstract
MicroRNAs (miRNAs) have important roles in various types of cellular biological processes. Our study aimed to determine whether miRNAs function in the regulation of ionizing radiation (IR)-induced cell death in auditory cells and to determine how they affect the cellular response to IR. Microarray and qRT-PCR were performed to identify and confirm the differential expression of miRNAs in the cochlea hair cell line HEI-OC1 and in vivo after IR. Upregulation or downregulation of miRNAs using miRNA mimics or inhibitor were detected to characterize the biological effects of the indicated miRNAs. Bioinformatic analyses, luciferase reporter assays and mRNA knockdown were performed to identify a miRNA target gene. We determined that miR-207 was significantly upregulated after IR. MiR-207 enhances IR-induced apoptosis and DNA damage in HEI-OC1 cells. Furthermore, Akt3 was confirmed to be a direct target of miR-207. Downregulation of Akt3 mimics the effects of miR-207. MiR-207 enhances IR-induced apoptosis by directly targeting Akt3 and anti-miR-207 may have a potential role in protecting cochlea hair cells from IR.
   

  Human OneArray  
 BioMed Research International. 2014 Sep 8.
 Gene Expression Profiling of Biological Pathway Alterations by Radiation Exposure
 
 
 Kuei-Fang Lee, Julia Tzu-Ya Weng, Paul Wei-Che Hsu, Yu-Hsiang Chi, Ching-Kai Chen, Ingrid Y. Liu, Yi-Cheng Chen, Lawrence Shih-Hsin Wu
  Abstract
Though damage caused by radiation has been the focus of rigorous research, the mechanisms through which radiation exerts harmful effects on cells are complex and not well-understood. In particular, the influence of low dose radiation exposure on the regulation of genes and pathways remains unclear. In an attempt to investigate the molecular alterations induced by varying doses of radiation, a genome-wide expression analysis was conducted. Peripheral blood mononuclear cells were collected from five participants and each sample was subjected to 0.5 Gy, 1 Gy, 2.5 Gy, and 5 Gy of cobalt 60 radiation, followed by array-based expression profiling. Gene set enrichment analysis indicated that the immune system and cancer development pathways appeared to be the major affected targets by radiation exposure. Therefore, 1 Gy radioactive exposure seemed to be a critical threshold dosage. In fact, after 1 Gy radiation exposure, expression levels of several genes including FADD, TNFRSF10B, TNFRSF8, TNFRSF10A, TNFSF10, TNFSF8, CASP1, and CASP4 that are associated with carcinogenesis and metabolic disorders showed significant alterations. Our results suggest that exposure to low-dose radiation may elicit changes in metabolic and immune pathways, potentially increasing the risk of immune dysfunctions and metabolic disorders.
   

  Human miRNA OneArray  
 BioMed Research International. 2014 Sep 16.
 MicroRNA Expression Profiling Altered by Variant Dosage of Radiation Exposure
 
 
 Kuei-Fang Lee, Yi-Cheng Chen, Paul Wei-Che Hsu, Ingrid Y. Liu, Lawrence Shih-Hsin Wu
  Abstract
Various biological effects are associated with radiation exposure. Irradiated cells may elevate the risk for genetic instability, mutation, and cancer under low levels of radiation exposure, in addition to being able to extend the postradiation side effects in normal tissues. Radiation-induced bystander effect (RIBE) is the focus of rigorous research as it may promote the development of cancer even at low radiation doses. Alterations in the DNA sequence could not explain these biological effects of radiation and it is thought that epigenetics factors may be involved. Indeed, some microRNAs (or miRNAs) have been found to correlate radiation-induced damages and may be potential biomarkers for the various biological effects caused by different levels of radiation exposure. However, the regulatory role that miRNA plays in this aspect remains elusive. In this study, we profiled the expression changes in miRNA under fractionated radiation exposure in human peripheral blood mononuclear cells. By utilizing publicly available microRNA knowledge bases and performing cross validations with our previous gene expression profiling under the same radiation condition, we identified various miRNA-gene interactions specific to different doses of radiation treatment, providing new insights for the molecular underpinnings of radiation injury.
   

  Human OneArray  
 Journal of Hazardous Materials. 2013 Nov 20;264C:303-312. doi: 10.1016/j.jhazmat.2013.11.031.
 Differential cytotoxic effects of gold nanoparticles in different mammalian cell lines
 
 
 linesPin Ju Chueh, Ruei-Yue Liang, Yi-Hui Lee, Zih-Ming Zeng, Show-Mei Chuang
  Abstract
Gold nanoparticles (AuNPs) possess unique properties that have been exploited in several medical applications. However, a more comprehensive understanding of the environmental safety of AuNPs is imperative for use of these nanomaterials. Here, we describe the impacts of AuNPs in various mammalian cell models using an automatic and dye-free method for continuous monitoring of cell growth based on the measurement of cell impedance. Several well-established cytotoxicity assays were also used for comparison. AuNPs induced a concentration-dependent decrease in cell growth. This inhibitory effect was associated with apoptosis induction in Vero cells but not in MRC-5 or NIH3T3 cells. Interestingly, cDNA microarray analyses in MRC-5 cells supported the involvement of DNA damage and repair responses, cell-cycle regulation, and oxidative stress in AuNP-induced cytotoxicity and genotoxicity. Moreover, autophagy appeared to play a role in AuNPs-induced attenuation of cell growth in NIH3T3 cells. In this study, we present a comprehensive overview of AuNP-induced cytotoxicity in a variety of mammalian cell lines, comparing several cytotoxicity assays. Collectively, these assays offer convincing evidence of the cytotoxicity of AuNPs and support the value of a systematic approach for analyzing the toxicology of nanoparticles.
   

  Human OneArray  
 Biochimica et Biophysica Acta-General Subjects. 2013 Jun 27. doi: 10.1016/j.bbagen.2013.06.025.
 Extensive evaluations of the cytotoxic effects of gold nanoparticles
 
 
 Show-Mei Chuang, Yi-Hui Lee, Ruei-Yue Liang, Gwo-Dong Roam, Zih-Ming Zeng, Hsin-Fang Tu, Shi-Kwun Wang, Pin Ju Chueh
  Abstract
Background: Many in vitro studies have revealed that the interference of dye molecules in traditional nanoparticle cytotoxicity assays results in controversial conclusions. The aim of this study is to establish an extensive and systematic method for evaluating biological effects of gold nanoparticles in mammalian cell lines. Methods: We establish the cell-impedance measurement system, a label-free, real-time cell monitoring platform that measures electrical impedance, displaying results as cell index values, in a variety of mammalian cell lines. Cytotoxic effects of gold nanoparticles are also evaluated with traditional in vitro assays. Results: Among the six cell lines, gold nanoparticles induce a dose-dependent suppression of cell growth with different levels of severity and the suppressive effect of gold nanoparticles was indirectly associated with their sizes and cellular uptake. Mechanistic studies revealed that the action of gold nanoparticles is mediated by apoptosis induction or cell cycle delay, depending on cell type and cellular context. Although redox signaling is often linked to the toxicity of nanoparticles, in this study, we found that gold nanoparticle-mediated reactive oxygen species generation was not sustained to notably modulate proteins involved in antioxidative defense system. Conclusion: The cell-impedancemeasurement system, a dye-free, real-time screening platform, provides a reliable analysis for monitoring gold nanoparticle cytotoxicity in a variety of mammalian cell lines. Furthermore, gold nanoparticles induce cellular signaling and several sets of gene expression tomodulate cellular physical processes. General significance: The systematic approach, such as cell-impedance measurement, analyzing the toxicology of nanomaterials offers convincing evidence of the cytotoxicity of gold nanomaterials.
   

  Human OneArray  
 ACS Nano. 2011, 5(12):9354-69. doi: 10.1021/nn2027775.
 Identification of the Nanogold Particle-Induced Endoplasmic Reticulum Stress by Omic Techniques and Systems Biology Analysis
 
 
 Yen-Yin Tsai, Yi-HueiHuang, Ya-Li Chao, Kuang-Yu Hu, Li-Te Chin, Shiu-Huey Chou, Ai-Ling Hour, Yeong-DerYao, Chi-Shun Tu, Yao-Jen Liang, Cheng-YuhTsai, Hao-Yu Wu, Shan-WenTan, Han-Min Chen
  Abstract
Growth inhibition and apoptotic/necrotic phenotype was observed in nanogold particle (AuNP)-treated human chronic myelogenous leukemia cells. To elucidate the underlying cellular mechanisms, proteomic techniques including two-dimensional electrophoresis/mass spectrometry and protein microarrays were utilized to study the differentially expressed proteome and phosphoproteome, respectively. Systems biology analysis of the proteomic data revealed that unfolded protein-associated endoplasmic reticulum (ER) stress response was the predominant event. Concomitant with transcriptomic analysis using mRNA expression, microarrays show ER stress response in the AuNP-treated cells. The ER stress protein markers' expression assay unveiled AuNPs as an efficient cellular ER stress elicitor. Upon ER stress, cellular responses, including reactive oxygen species increase, mitochondrial cytochrome c release, and mitochondria damage, chronologically occurred in the AuNP-treated cells. Conclusively, this study demonstrates that AuNPs cause cell death through induction of unmanageable ER stress.
   

  Human OneArray  
 Chemical Research in Toxicology. 2011, 24(10):1636-43. doi: 10.1021/tx200181q.
 Whole Genome Expression in Peripheral-Blood Samples of Workers Professionally Exposed to Polycyclic Aromatic Hydrocarbons.
 
 
 Wu MT, Lee TC, Wu IC, Su HJ, Huang JL, Peng CY, Wang W, Chou TY, Lin MY, Lin WY, Huang CT, Pan CH, Ho CK.
  Abstract
This study aims to examine global gene expression profiles before and after the work-shift among coke-oven workers (COWs). COWs work six consecutive days and then take two days off. Two blood and urine samples in each worker were collected before starting to work after two days off and end-of-shift in the sixth day of work in 2009. Altered gene expressions (ratio of gene expression levels between end-of-shift and preshift work) were performed by a Human OneArray expression system which probes ~30,000-transcription expression profiling of human genes. Sixteen workers, all men, were enrolled in this study. Median urinary 1-hydroxypyrene (1OHP) levels (弮mol/mol creatinine) in end-of-shift work were significantly higher than those in preshift work (2.58 vs 0.29, p = 0.0002). Among the 20,341 genes which passed experimental quality control, 26 gene expression changes, 7 positive and 19 negative, were highly correlated with across-the-shift urinary 1OHP levels (end-of-shift-preshift 1OHP) (p-value <0.001). The high and low exposure groups of across-the-shift urinary 1OHP levels dichotomized in ~2.00 弮mol/mol creatinine were able to be distinguished by these 26 genes. Some of them are known to be involved in apoptosis, chromosome stability/DNA repair, cell cycle control/tumor suppressor, cell adhesion, development/spermatogenesis, immune function, and neuronal cell function. These findings in COWs will be an ideal model to study the relationship of PAH exposure with acute changes of gene expressions.
   

  Human OneArray  
 Libertas Academica. 2011, 6:7-16.
 Aberrantly Expressed Genes in HaCaT Keratinocytes Chronically Exposed to Arsenic Trioxide
 
 
 Udensi K. Udensi, Hari H.P. Cohly, Barbara E. Graham-Evans, Kenneth Ndebele, Nat?lia Garcia-Reyero, Bindu Nanduri, Paul B. Tchounwou, Raphael D. Isokpehi.
  Abstract
Inorganic arsenic is a known environmental toxicant and carcinogen of global public health concern. Arsenic is genotoxic and cytotoxic to human keratinocytes. However, the biological pathways perturbed in keratinocytes by low chronic dose inorganic arsenic are not completely understood. The objective of the investigation was to discover the mechanism of arsenic carcinogenicity in human epidermal keratinocytes. We hypothesize that a combined strategy of DNA microarray, qRT-PCR and gene function annotation will identify aberrantly expressed genes in HaCaT keratinocyte cell line after chronic treatment with arsenic trioxide. Microarray data analysis identified 14 up-regulated genes and 21 down-regulated genes in response to arsenic trioxide. The expression of 4 up-regulated genes and 1 down-regulated gene were confirmed by qRT-PCR. The up-regulated genes were AKR1C3 (Aldo-Keto Reductase family 1, member C3), IGFL1 (Insulin Growth Factor-Like family member 1), IL1R2 (Interleukin 1 Receptor, type 2), and TNFSF18 (Tumor Necrosis Factor [ligand] SuperFamily, member 18) and down-regulated gene was RGS2 (Regulator of G-protein Signaling 2). The observed over expression of TNFSF18 (167 fold) coupled with moderate expression of IGFL1 (3.1 fold), IL1R2 (5.9 fold) and AKR1C3 (9.2 fold) with a decreased RGS2 (2.0 fold) suggests that chronic arsenic exposure could produce sustained levels of TNF with modulation by an IL-1 analogue resulting in chronic immunologic insult. A concomitant decrease in growth inhibiting gene (RGS2) and increase in AKR1C3 may contribute to chronic inflammation leading to metaplasia, which may eventually lead to carcinogenicity in the skin keratinocytes. Also, increased expression of IGFL1 may trigger cancer development and progression in HaCaT keratinocytes.
   

  Human OneArray  
 Nanotechnology. 2010, 21(23):235103. doi: 10.1088/0957-4484/21/23/235103.
 Homologous RBC-derived vesicles as ultrasmall carriers of iron oxide for magnetic resonance imaging of stem cells
 
 
 Microsugar Chang, Jong-Kai Hsiao, Ming Yao, Li-Ying Chien, Szu-Chun Hsu, Bor-Sheng Ko, Shin-Tai Chen, Hon-Man Liu, Yao-Chang Chen, Chung-Shi Yang, Dong-Ming Huang
  Abstract
Ultrasmall superparamagnetic iron oxide (USPIO) particles are very useful for cellular magnetic resonance imaging (MRI), which plays a key role in developing successful stem cell therapies. However, their low intracellular labeling efficiency, and biosafety concerns associated with their use, have limited their potential usage. In this study we develop a novel system composed of RBC-derived vesicles (RDVs) for efficient delivery of USPIO particles into human bone marrow mesenchymal stem cells (MSCs) for cellular MRI in vitro and in vivo. RDVs are highly biosafe to their autologous MSCs as manifested by cell viability, differentiation, and gene microarray assays. The data demonstrate the potential of RDVs as intracellular delivery vehicles for biomedical applications.
   

  Human OneArray  
 Clin Transl Sci. 2010, 3(4):158-69. doi: 10.1111/j.1752-8062.2010.00212.x.
 A New Class of Human Mast Cell and Peripheral Blood Basophil Stabilizers that Differentially Control Allergic Mediator Release
 
 
 Sarah K. Norton, Anthony Dellinger, Zhiguo Zhou, Robert Lenk, Darren MacFarland, Becky Vonakis, Daniel Conrad, Christopher L. Kepley
  Abstract
Treatments for allergic disease block the effects of mediators released from activated mast cells and blood basophils. A panel of fullerene derivatives was synthesized and tested for their ability to preempt the release of allergic mediators in vitro and in vivo. The fullerene C(70)-tetraglycolic acid significantly inhibited degranulation and cytokine production from mast cells and basophils, while C(70)-tetrainositol blocked only cytokine production in mast cells and degranulation and cytokine production in basophils. The early phase of FcepsilonRI inhibition was dependent on the blunted release of intracellular calcium stores, elevations in reactive oxygen species, and several signaling molecules. Gene microarray studies further showed the two fullerene derivatives inhibited late phase responses in very different ways. C(70)-tetraglycolic acid was able to block mast cell-driven anaphylaxis in vivo, while C(70)-tetrainositol did not. No toxicity was observed with either compound. These findings demonstrate the biological effects of fullerenes critically depends on the moieties added to the carbon cage and suggest they act on different FcepsilonRI-specific molecules in mast cells and basophils. These next generation fullerene derivatives represent a new class of compounds that interfere with FcepsilonRI signaling pathways to stabilize mast cells and basophils. Thus, fullerene-based therapies may be a new approach for treating allergic diseases.
   

  Human OneArray  
 Acta Pharmacol Sin. 2010, 31(2):227-36. doi: 10.1038/aps.2009.197.
 Microarray analysis reveals the inhibition of nuclear factor-kappa B signaling by aristolochic acid in normal human kidney (HK-2) cells
 
 
 Chen YY, Chiang SY, Wu HC, Kao ST, Hsiang CY, Ho TY, Lin JG.
  Abstract
To study the molecular mechanism underlying the effect of aristolochic acid (AA), a major active component of plants from the Aristolochiaceae family using microarray analysis. Human kidney (HK-2) cells were treated with AA (0, 10, 30, and 90 micromol/L) for 24 h, and the cell viability was measured by a 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazolium bromide assay. Complementary DNA microarrays were used to investigate the gene expression pattern of HK-2 cells exposed to AA in triplicate. A quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay was used to verify the microarray data for selected nuclear factor kappa B (NF-kappaB)-regulated genes. Furthermore, the subcellular localization of NF-kappaB p65 was visualized by immunofluorescence confocal microscopy in HK-2 cells. The NF-kappaB activity was examined by a luciferase reporter assay in HK-2/NF-kappaB transgenic cells. AA exhibited a dose-dependent cytotoxic effect in HK-2 cells and induced alterations in the gene expression profiles related to the DNA damage response, DNA repair, macromolecule metabolic process, carbohydrate metabolic process, DNA metabolic process, apoptosis, cell cycle, and transcription. In addition, 9 biological pathways associated with immunomodulatory functions were down-regulated in AA-treated HK-2 cells. A network analysis revealed that NF-kappaB played a central role in the network topology. Among NF-kappaB-regulated genes, 8 differentially expressed genes were verified by qRT-PCR. The inhibition of NF-kappaB activity by AA was further confirmed by immunofluorescence confocal microscopy and by NF-kappaB luciferase reporter assay. Our data revealed that AA could suppress NF-kappaB activity in normal human cells, perhaps partially accounting for the reported anti-inflammatory effects of some plants from the genus Aristolochia.
   

  Mouse OneArray  
 Journal of Environmental Science and Health. 2010, 28(1):60-87. doi: 10.1080/10590500903585416.
 Gene Expression Profiling as an Initial Approach for Mechanistic Studies of Toxicity and Tumorigenicity of Herbal Plants and Herbal Dietary Supplements.
 
 
 Nan Mei, Qingsu Xia, Tao Chen, Po-Chuen Chan, Peter P. Fu, Lei Guo
  Abstract
Dietary supplements are consumed by more than 300 million people worldwide, and herbal dietary supplements represent the most rapidly growing portion of this industry. Even though adverse health effects of many herbal dietary supplements have been reported, safety assurances are not being addressed adequately. Toxicological data on the identification of genotoxic and tumorigenic ingredients in many raw herbs are also lacking. Currently, more than 30 herbal dietary supplements and active ingredients have been selected by the National Toxicology Program (NTP) for toxicity and tumorigenicity studies. Due to the complexity of the chemical components present in plant extracts, there are no established methodologies for determining the mechanisms of toxicity (particularly tumorigenicity) induced by herbs, such as Gingko biloba leaf extract (GBE) and other herbal plant extracts. Consequently, the understanding of toxicity of herbal dietary supplements remains limited. We have proposed that application of DNA microarrays could be a highly practical initial approach for revealing biological pathways and networks associated with toxicity induced by herbal dietary supplements and the generation of hypotheses to address likely mechanisms. The changes in expression of subsets of genes of interest, such as the modulation of drug metabolizing genes, can be analyzed after treatment with an herbal dietary supplement. Although levels of gene expression do not represent fully the levels of protein activities, we propose that subsequent biochemical and genomic experiments based on these initial observations will enable elucidation of the mechanisms leading to toxicity, including tumorigenicity. This review summarizes the current practices of microarray analysis of gene expressions in animals treated with herbal dietary supplements and discusses perspectives for the proposed strategy.
   

  Human OneArray  
 Ind Health. 2011, 49(1):8-14.
 Changes in Oxidative Stress Biomarker and Gene Expression Levels in Workers Exposed to Volatile Organic Compounds.
 
 
 Kim JH, Moon JY, Park EY, Lee KH, Hong YC.
  Abstract
Exposure to volatile organic compounds (VOCs) was known to result in immunologic, respiratory, carcinogenic, reproductive, neurologic, and cardiovascular effects. However, the mechanisms by which VOCs induce these adverse health effects are not well understood. To evaluate the change of oxidative stress biomarker and gene expression levels in workers exposed to VOCs, we obtained urine and blood samples from 21 subjects before and after occupational exposure to VOCs. We measured levels of muconic acid (MuA), hippuric acid (HA), mandelic acid (MaA), and methyl hippuric acid (MHA) as urinary exposure biomarkers for benzene, toluene, ethylbenzene, and xylene (collectively BTEX), and malondialdehyde (MDA) and 8-hydroxydeoxyguanine (8-OHdG) as oxidative stress biomarkers in all subjects. We also evaluated BTEX-mediated RNA expression using cDNA microarray in 14 subjects. HA and MHA levels were higher following occupational exposure to VOCs (p < 0.01). In the linear regression analysis, HA ratios of after- and before-exposure were found to be significantly associated with increase of MDA ratios of after- and before-exposure after controlling for age, body mass index, and smoking (帣 = 0.06, p = 0.031). Evaluation of the gene expressions by HA showed that 23 gene expressions were found to be significantly associated with HA levels after adjusting for age, body mass index, and smoking (p < 0.001). In particular, expressions of ENO3 and CDNA FLJ39461 fis among the 23 genes were significantly associated with the change in MDA level (p < 0.05). Our study results suggest that exposure to VOCs, specifically toluene, induces oxidative stress and various gene expression change of which some may be responsible for oxidative stress.
   

  Mouse OneArray  
 Journal of Ethnopharmacology. 2010, 132(2):429-37. doi: 10.1016/j.jep.2010.08.022.
 Application of bioactivity database of Chinese herbal medicine on the therapeutic prediction, drug development, and safety evaluation.
 
 
 Cheng HM, Li CC, Chen CY, Lo HY, Cheng WY, Lee CH, Yang SZ, Wu SL, Hsiang CY, Ho TY.
  Abstract
Chinese herbal medicine has been used for the treatments of various diseases for years. However, it is often difficult to analyze their biological activities and molecule mechanisms because of their complex nature. In this study, we applied DNA microarray to analyze the biological events induced by herbal formulae, predict the therapeutic potentials of formulae, and evaluate the safety of formulae. Mice were administrated orally with 15 formulae for 7 consecutive days, and the gene expression profiles in liver or kidney were further analyzed by transcriptomic tools. Our data showed that most formulae altered the metabolic pathways, such as glutathione metabolism and oxidative phosphorylation, and regulatory pathways, such as antigen processing and presentation and insulin-like growth factor signaling pathway. By comparing the gene expression signatures of formulae with those of disease states or drugs, we found that mice responsive to formula treatments might be related to disease states, especially metabolic and cardiovascular diseases, and drugs, which exhibit anti-cancer, anti-inflammatory, and anti-oxidative effects. Moreover, most formulae altered the expression levels of cytochrome p450, glutathione S-transferase, and UDP glycosyltransferase genes, suggesting that caution should be paid to possible drug interaction of these formulae. Furthermore, the similarities of gene expression profiles between formulae and toxic chemicals were low in kidney, suggesting that these formulae might not induce nephrotoxicities in mice. This report applied transcriptomic tools as a novel platform of translational medicine for Chinese herbal medicine. This platform will not only for understanding the therapeutic mechanisms involving herbal formulae and gene interactions, but also for the new theories in drug discovery.
   

  Mouse OneArray  
 Nanotechnology. 2010, 21(17):175101. doi: 10.1088/0957-4484/21/17/175101.
 Long-term hepatotoxicity of polyethylene-glycol functionalized multi-walled carbon nanotubes in mice.
 
 
 Zhang D, Deng X, Ji Z, Shen X, Gu T, Liu Y, Dong L, Wu M
  Abstract
The toxicity of polyethylene-glycol functionalized (PEGylated) multi-walled carbon nanotubes (MWCNTs) and non-PEGylated MWCNTs in vivo was evaluated and compared. Mice were exposed to MWCNTs by intravenous injection. The activity level of glutathione, superoxide dismutase and gene expression in liver, as well as some biochemical parameters and the tumor necrosis factor alpha level in blood were measured over 2 months. The pathological and electron micrographic observations of liver evidently indicate that the damage caused by non-PEGylated MWCNTs is slightly more severe than that of PEGylated MWCNTs, which means that PEGylation can partly, but not substantially, improve the in vivo biocompatibility of MWCNTs.
   

  Mouse OneArray  
 Nanotechnology. 2009, 20(44):445101. doi: 10.1088/0957-4484/20/44/445101.
 The hepatotoxicity of multi-walled carbon nanotubes in mice
 
 
 Zongfei Ji, Danying Zhang, Ling Li, Xizhong Shen, Minhong Wu, Yuanfang Liu, Xiaoyong Deng, Ling Dong
  Abstract
The hepatotoxicity of two types of multi-walled carbon nanotubes (MWCNTs), acid-oxidized MWCNTs (O-MWCNTs) and Tween-80-dispersed MWCNTs (T-MWCNTs), were investigated with Kunming mice exposed to 10 and 60 mg kg(-1) by intravenous injection for 15 and 60 d. Compared with the PBS group, the body-weight gain of the mice decreased and the level of total bilirubin and aspartate aminotransferase increased in the MWCNT-exposed group with a significant dose-effect relationship, while tumor necrosis factor alpha level did not show significant statistical change within 60 d. Spotty necrosis, inflammatory cell infiltration in portal region, hepatocyte mitochondria swelling and lysis were observed with a significant dose-effect relationship in the MWCNT groups. Liver damage of the T-MWCNT group was more severe than that of the O-MWCNT group according to the Roenigk classification system. Furthermore, T-MWCNTs induce slight liver oxidative damage in mice at 15 d, which was recovered at 60 d. Part of the gene expressions of mouse liver in the MWCNT groups changed compared to the PBS group, including GPCRs (G protein-coupled receptors), cholesterol biosynthesis, metabolism by cytochrome P450, natural-killer-cell-mediated cytotoxicity, TNF- alpha, NF-kappaB signaling pathway, etc. In the P450 pathway, the gene expressions of Gsta2 (down-regulated), Cyp2B19 (up-regulated) and Cyp2C50 (down-regulated) had significant changes in the MWCNT groups. These results show that a high dose of T-MWCNTs can induce hepatic toxicity in mice while O-MWCNTs seem to have less toxicity.
   

  Mouse OneArray  
 Biomaterials. 2009, 30(17):3042-9. doi: 10.1016/j.biomaterials.2009.02.016.
 Nuclear factor-kB bioluminescence imaging-guided transcriptomic analysis for the assessment of hostbiomaterial interaction in vivo.
 
 
 Hsiang CY, Chen YS, Ho TY.
  Abstract
Establishment of a comprehensive platform for the assessment of host-biomaterial interaction in vivo is an important issue. Nuclear factor-kappaB (NF-kappaB) is an inducible transcription factor that is activated by numerous stimuli. Therefore, NF-kappaB-dependent luminescent signal in transgenic mice carrying the luciferase genes was used as the guide to monitor the biomaterials-affected organs, and transcriptomic analysis was further applied to evaluate the complex host responses in affected organs in this study. In vivo imaging showed that genipin-cross-linked gelatin conduit (GGC) implantation evoked the strong NF-kappaB activity at 6h in the implanted region, and transcriptomic analysis showed that the expressions of interleukin-6 (IL-6), IL-24, and IL-1 family were up-regulated. A strong luminescent signal was observed in spleen on 14 d, suggesting that GGC implantation might elicit the biological events in spleen. Transcriptomic analysis of spleen showed that 13 Kyoto Encyclopedia of Genes and Genomes pathways belonging to cell cycles, immune responses, and metabolism were significantly altered by GGC implants. Connectivity Map analysis suggested that the gene signatures of GGC were similar to those of compounds that affect lipid or glucose metabolism. GeneSetTest analysis further showed that host responses to GGC implants might be related to diseases states, especially the metabolic and cardiovascular diseases. In conclusion, our data provided a concept of molecular imaging-guided transcriptomic platform for the evaluation and the prediction of host-biomaterial interaction in vivo.
   

  Mouse OneArray  
 Environmental and Molecular Mutagenesis. 2008, 49(9):741-5. doi: 10.1002/em.20429.
 Gene Expression Changes Associated with Xenobiotic Metabolism Pathways in Mice Exposed to Acrylamide.
 
 
 Guo L, Tseng J, Dial SL, Liao W, Manjanatha MG, Mei N
  Abstract
The discovery of acrylamide (AA) in a variety of fried foods has raised public health concerns. In this study, groups of male mice were administered 500 mg/L AA in drinking water for 3 weeks, and gene expression changes were evaluated in the livers of AA-treated mice within 24 hr of the last treatment. When a two-fold cutoff value and a P-value less than 0.05 were selected, 696 genes (233 up-regulated and 463 down-regulated) were identified as differentially expressed genes in AA-treated mice when compared with the controls. Gene ontology analysis revealed that the principle pathways affected by AA were xenobiotic metabolism by cytochrome P450 (CYPs) and glutathione metabolism, suggesting that drug and/or xenobiotic metabolism is most affected by exposure. The results provide more information about AA metabolism and further insight into the molecular mechanisms involved in AA-induced toxicity.