51
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Cho YE, Moon PG, Lee JE, Singh TSK, Kang W, Lee HC, Lee MH, Kim SH, Baek MC. Integrative analysis of proteomic and transcriptomic data for identification of pathways related to simvastatin-induced hepatotoxicity. Proteomics 2013; 13:1257-75. [PMID: 23322611 DOI: 10.1002/pmic.201200368] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 10/10/2012] [Accepted: 11/06/2012] [Indexed: 01/12/2023]
Abstract
Hepatocytes are used widely as a cell model for investigation of xenobiotic metabolism and the toxic mechanism of drugs. Simvastatin is the first statin drug used extensively in clinical practice for control of elevated cholesterol or hypercholesterolemia. However, it has also been reported to cause adverse effects in liver due to cellular damage. In this study, for proteomic and transcriptomic analysis, rat primary hepatocytes were exposed to simvastatin at IC20 concentration for 24 h. Among a total of 607 differentially expressed proteins, 61 upregulated and 29 downregulated proteins have been identified in the simvastatin-treated group. At the mRNA level, results of transcriptomic analysis revealed 206 upregulated and 41 downregulated genes in the simvastatin-treated group. Based on results of transcriptomic and proteomic analysis, NRF2-mediated oxidative stress response, xenobiotics by metabolism of cytochrome P450, fatty acid metabolism, bile metabolism, and urea cycle and inflammation metabolism pathways were focused using IPA software. Genes (FASN, UGT2B, ALDH1A1, CYP1A2, GSTA2, HAP90, IL-6, IL-1, FABP4, and ABC11) and proteins (FASN, CYP2D1, UG2TB, ALDH1A1, GSTA2, HSP90, FABP4, and ABCB11) related to several important pathways were confirmed by real-time PCR andWestern blot analysis, respectively. This study will provide new insight into the potential toxic pathways induced by simvastatin.
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Affiliation(s)
- Young-Eun Cho
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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52
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Huang Q, Zhang J, Peng S, Tian M, Chen J, Shen H. Effects of water soluble PM2.5 extracts exposure on human lung epithelial cells (A549): A proteomic study. J Appl Toxicol 2013; 34:675-87. [DOI: 10.1002/jat.2910] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/21/2013] [Accepted: 06/12/2013] [Indexed: 12/20/2022]
Affiliation(s)
- Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 People's Republic of China
| | - Jie Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 People's Republic of China
| | - Siyuan Peng
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 People's Republic of China
| | - Meiping Tian
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 People's Republic of China
| | - Jinsheng Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 People's Republic of China
| | - Heqing Shen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment; Chinese Academy of Sciences; Xiamen 361021 People's Republic of China
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53
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Lionetto L, Gentile G, Bellei E, Capi M, Sabato D, Marsibilio F, Simmaco M, Pini LA, Martelletti P. The omics in migraine. J Headache Pain 2013; 14:55. [PMID: 23815568 PMCID: PMC3727988 DOI: 10.1186/1129-2377-14-55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/22/2013] [Indexed: 12/29/2022] Open
Abstract
The term omics consist of three main areas of molecular biology, such as genomics, proteomics and metabolomics. The omics synergism recognise migraine as an ideal study model, due to its multifactorial nature. In this review, the plainly research data featuring in this complex network are reported and analyzed, as single or multiple factor in pathophysiology of migraine. The future of migraine biomolecular research shall be focused on networking among these different and hierarchical disciplines. We have to look for its Ariadne’s tread, in order to see the whole painting of migraine molecular biology.
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Affiliation(s)
- Luana Lionetto
- Sant'Andrea Hospital, Advanced Molecular Diagnostics Unit, Via di Grottarossa 1035 - 1039, Rome 00189, Italy.
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54
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Hassan NS, Abdelkawi SA. Assessing of plasma protein denaturation induced by exposure to cadmium, electromagnetic fields and their combined actions on rat. Electromagn Biol Med 2013; 33:147-53. [DOI: 10.3109/15368378.2013.800101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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55
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George J, Shukla Y. Early changes in proteome levels upon acute deltamethrin exposure in mammalian skin system associated with its neoplastic transformation potential. J Toxicol Sci 2013; 38:629-42. [DOI: 10.2131/jts.38.629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Jasmine George
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), India
| | - Yogeshwer Shukla
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), India
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56
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Rasaputra KS, Liyanage R, Lay, Jr JO, Slavik MF, Rath NC. Effect of thiram on avian growth plate chondrocytes in culture. J Toxicol Sci 2013; 38:93-101. [DOI: 10.2131/jts.38.93] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Komal Singh Rasaputra
- Department of Poultry Science, University of Arkansas
- Agricultural Research Service/ USDA, Poultry Science Center, University of Arkansa
| | - Rohana Liyanage
- State Wide Mass Spectrometry Facility, University of Arkansas
| | | | | | - Narayan C. Rath
- Agricultural Research Service/ USDA, Poultry Science Center, University of Arkansa
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57
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Liu F, Wang WX. Proteome pattern in oysters as a diagnostic tool for metal pollution. JOURNAL OF HAZARDOUS MATERIALS 2012; 239-240:241-8. [PMID: 22999020 DOI: 10.1016/j.jhazmat.2012.08.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 05/20/2023]
Abstract
The present study investigated whether proteome pattern of an oyster Crassostrea hongkongensis could be used as a diagnostic tool for contamination and toxicity of metals/metalloids in a real multiple metal-contaminated estuary. We collected oysters along a pollution gradient from highly contaminated to relatively clean sites. The oysters showed distinct contamination gradients of Cu, Zn and Cd. Proteomic analysis of the oyster gills as one of major metal targets identified a proteome pattern composed of 13 commonly altered proteins in the contaminated oysters. The discovered proteome pattern completely segregated the contaminated from the clean individuals, and the pattern achieved clear classification of the oysters with different contamination levels. Importantly, the integrated changes of gill proteome were linearly related to the integrated contamination of the metal mixtures present in oyster tissues. It is suggested that proteome pattern is a promising diagnostic tool for metal pollution assessment in environmental monitoring programs.
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Affiliation(s)
- Fengjie Liu
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong
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58
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Cho YE, Kim SH, Baek MC. Proteome profiling of tolbutamide-treated rat primary hepatocytes using nano LC-MS/MS and label-free protein quantitation. Electrophoresis 2012; 33:2806-17. [PMID: 22911336 DOI: 10.1002/elps.201200193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/10/2012] [Accepted: 05/15/2012] [Indexed: 11/06/2022]
Abstract
Tolbutamide is used as a first line oral antihyperglycemic drug for type 2 diabetes. One side effect of this drug, hepatotoxicity, is well recognized; however, the precise mechanisms underlying tolbutamide-induced hepatotoxicity remain unclear. In this respect, proteomics techniques were used to gain further insight into the mechanistic processes of the hepatotoxicity induced by this drug. In this study, we aimed to identify molecular pathways based on proteins responding to cellular toxicity in tolbutamide-treated primary hepatocytes, using nano UPLC-MS/MS analysis. Rat primary hepatocytes were treated with an IC(20) concentration for 24 h to study the hepatotoxic effects of tolbutamide. For high-throughput label-free quantitation, tryptic-digested peptides of proteins from cell lysates were analyzed using LC-MS/MS and quantitated using the IDEAL-Q software, in which several parameters, such as assisted sequence, elution time, and mass-to-charge ratio were included. We quantified a total of 330 distinct proteins from the tolbutamide-treated hepatocytes and identified 55 upregulated and 82 downregulated proteins with expression changes. Among these differentially expressed proteins, we focused mainly on the 18 upregulated proteins belonging to xenobiotic cytochrome P450 (CYP), drug metabolism/detoxification, oxidative stress/antioxidant response, and cell damage pathway. CYP2D1, CYP2C11, UDP-glucuronosyltransferase 2B (UGT2B), superoxide dismutase 2 (SOD2), 60 kDa heat shock protein (HSPD1), heat shock protein 90 (HSP90), and catalase (CAT) were confirmed by Western blot analysis. In addition, various xenobiotic CYP proteins upregulated in the tolbutamide-treated group, CYP2D1, CYP2C13, and CYP2C11 were confirmed by reverse transcriptase-PCR analysis. Our results offer important new insights into the molecular mechanisms of tolbutamide-induced hepatotoxicity.
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Affiliation(s)
- Young-Eun Cho
- Department of Molecular Medicine, Kyungpook National University, Daegu, Republic of Korea
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59
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Kolarcik C, Bowser R. Plasma and Cerebrospinal Fluid-Based Protein Biomarkers for Motor Neuron Disease. Mol Diagn Ther 2012; 10:281-92. [PMID: 17022691 DOI: 10.1007/bf03256203] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Motor neuron diseases (MNDs) and, in particular, amyotrophic lateral sclerosis (ALS), are a heterogeneous group of neurologic disorders characterized by the progressive loss of motor function. In ALS, a selective and relentless degeneration of both upper and lower motor neurons occurs, culminating in mortality typically within 5 years of symptom onset. However, survival rates vary among individual patients and can be from a few months to >10 years from diagnosis. Inadequacies in disease detection and treatment, along with a lack of diagnostic and prognostic tools, have prompted many to turn to proteomics-based biomarker discovery efforts. Proteomics refers to the study of the proteins expressed by a genome at a particular time, and the proteome can respond to and reflect the status of an organism, including health and disease states. Although an emerging field, proteomic applications promise to uncover biomarkers critical for differentiating patients with ALS and other MNDs from healthy individuals and from patients affected by other diseases. Ideally, these studies will also provide mechanistic information to facilitate identification of new drug targets for subsequent therapeutic development. In addition to proper experimental design, standard operating procedures for sample acquisition, preprocessing, and storage must be developed. Biological samples typically analyzed in proteomic studies of neurologic diseases include both plasma and cerebrospinal fluid (CSF). Recent studies have identified individual proteins and/or protein panels from blood plasma and CSF that represent putative biomarkers for ALS, although many of these proteins are not unique to this disease. Continued investigations are required to validate these initial findings and to further pursue the role of these proteins as diagnostic biomarkers or surrogate markers of disease progression. Protein biomarkers specific to ALS will additionally function to evaluate drug efficacy in clinical trials and to identify novel targets for drug design. It is hoped that proteomic technologies will soon integrate the basic biology of ALS with mechanistic disease information to achieve success in the clinical setting.
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Affiliation(s)
- Christi Kolarcik
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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60
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Zhang W, Liu Y, Zhang H, Dai J. Proteomic analysis of male zebrafish livers chronically exposed to perfluorononanoic acid. ENVIRONMENT INTERNATIONAL 2012; 42:20-30. [PMID: 21481936 DOI: 10.1016/j.envint.2011.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 01/29/2011] [Accepted: 03/02/2011] [Indexed: 05/27/2023]
Abstract
Perfluorononanoic acid (PFNA), a synthetic perfluorinated carboxylic acid and fluorosurfactant, is a known environmental contaminant found in people and wildlife. To understand the hepatotoxicity mechanism of PFNA, male zebrafish (n=200) were exposed to differing concentrations of PFNA (0, 0.1, 0.5, and 1.0 mg/L) for 180 days. A two-dimensional difference gel electrophoresis (2-D DIGE) approach coupled with MALDI-TOF-MS/MS analysis was employed to detect and identify the differential expressed proteins. A total of 57 proteins were successfully identified and categorized into functional classes that included metabolism (amino acid metabolism, TCA cycle and pyruvate metabolism, gluconeogenesis and glycolysis, protein metabolism and modification, and nucleotides metabolism), structure and motility, stress and defense, signal transduction, and cell communication. Our proteomic analyses added new perspective to PFNA hepatotoxicity in zebrafish. Results regarding mRNA levels demonstrated that the involvement of peroxisome proliferator-activated receptors (PPARs) could not sufficiently explain the hepatotoxicity mechanism of PFAAs in zebrafish. The extensive protein variations indicated that multiple cellular pathways were involved in and suggested that multiple protein molecules should be simultaneously targeted as an effective strategy to counter PFNA toxicity. Other potential modes should be further investigated.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
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61
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Fornander L, Ghafouri B, Lindahl M, Graff P. Airway irritation among indoor swimming pool personnel: trichloramine exposure, exhaled NO and protein profiling of nasal lavage fluids. Int Arch Occup Environ Health 2012; 86:571-80. [DOI: 10.1007/s00420-012-0790-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 06/11/2012] [Indexed: 11/30/2022]
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62
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Huang X, Huang HQ. Alteration of the kidney membrane proteome of Mizuhopecten yessoensis induced by low-level methyl parathion exposure. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2012; 114-115:189-199. [PMID: 22446831 DOI: 10.1016/j.aquatox.2012.01.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 01/25/2012] [Accepted: 01/31/2012] [Indexed: 05/31/2023]
Abstract
Methyl parathion (MP) is a widely used organophosphorus pesticide that causes severe health and environmental effects. We investigated the alteration of the proteomic profile in the membrane enriched fraction of the kidneys of the scallop Mizuhopecten yessoensis exposed to low-level MP. Gas chromatography analysis showed that MP residues were significantly accumulated in the kidneys and the digestive glands of the scallops. According to two-dimensional electrophoresis, 17 proteins were differentially modulated under MP exposure. The mRNA expressions of 12 differential proteins were analyzed using quantitative PCR, and 10 showed consistent alteration of mRNA level with that of protein expression level. Altered expressions of two proteins (mitochondrial processing peptidase and α-tubulin) were also examined using Western blotting, showing that the mitochondrial processing peptidase was down-regulated but α-tubulin remained unchanged in response to MP exposure. Subcellular locations of all the identified proteins that were predicted using bioinformatics tools indicate that few of them are permanently located in the membrane. The differentially expressed proteins are involved in several critical biological processes, and their relevance to human health has been illuminated. These data taken together have provided some novel insights into the chronic toxicity mechanism of MP and have suggested mitochondrial processing peptidase as a potential biomarker for human health and environmental monitoring.
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Affiliation(s)
- Xiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, China
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63
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Van Summeren A, Renes J, van Delft JH, Kleinjans JC, Mariman EC. Proteomics in the search for mechanisms and biomarkers of drug-induced hepatotoxicity. Toxicol In Vitro 2012; 26:373-85. [DOI: 10.1016/j.tiv.2012.01.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/22/2011] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
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64
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Phark S, Park SY, Choi S, Zheng Z, Cho E, Lee M, Lim JY, Seo JB, Won NH, Jung WW, Sul D. Toxicological biomarkers of 2,3,4,7,8-pentachlorodibenzofuran in proteins secreted by HepG2 cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:656-66. [DOI: 10.1016/j.bbapap.2012.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/20/2012] [Accepted: 01/22/2012] [Indexed: 01/08/2023]
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65
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Zhu B, Gao KS, Wang KJ, Ke CH, Huang HQ. Gonad differential proteins revealed with proteomics in oyster (Saccostrea cucullata) using alga as food contaminated with cadmium. CHEMOSPHERE 2012; 87:397-403. [PMID: 22230729 DOI: 10.1016/j.chemosphere.2011.12.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 12/07/2011] [Accepted: 12/12/2011] [Indexed: 05/31/2023]
Abstract
As mercury and lead, cadmium (Cd) is one of the highly toxic metals in both the ocean and land environments, but its toxicological mechanism in organisms including human is still unclear because of the complex toxicological pathways in vivo. Here, the alga Chlorella vulgaris were cultivated at room temperature under the stress of cadmium (1 mg L(-1)) to obtain a toxic food, and then the contaminated food were directly supplied to oyster (Saccostrea cucullata) in seawater. After feeding with C. vulgaris contaminated with Cd (C. vulgaris-Cd), the differential proteins in the oyster gonad (OG) were effectively separated and identified with proteomic approaches. Eleven protein spots were observed to be significantly changed in the OG feeding with C. vulgaris-Cd, which seven spots of these differential proteins were down-regulated while four spots were up-regulated. These altered spots were further excised in gels and identified by a combined technique of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) and database searching. A portion of these differential proteins were further proofed by real-time PCR and Western blotting. The results indicate that the major functions of these differential proteins were described as follows: binding, protein translocation, catalysis, regulation of energy metabolism, reproductive function and skeleton structure. These differential proteins in part may effectively provide a few novel biomarkers for the evaluation of Cd pollution level via a food pathway for harming halobios, mammal and human health, and for understanding the complex mechanisms of Cd toxicity in vivo.
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Affiliation(s)
- Bo Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, China
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66
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Li G, Cai F, Yan W, Li C, Wang J. A Proteomic Analysis of MCLR-induced Neurotoxicity: Implications for Alzheimer's Disease. Toxicol Sci 2012; 127:485-95. [DOI: 10.1093/toxsci/kfs114] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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67
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Rusyn I, Sedykh A, Low Y, Guyton KZ, Tropsha A. Predictive modeling of chemical hazard by integrating numerical descriptors of chemical structures and short-term toxicity assay data. Toxicol Sci 2012; 127:1-9. [PMID: 22387746 DOI: 10.1093/toxsci/kfs095] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR-like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage.
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Affiliation(s)
- Ivan Rusyn
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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68
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George J, Shukla Y. Pesticides and cancer: Insights into toxicoproteomic-based findings. J Proteomics 2011; 74:2713-22. [DOI: 10.1016/j.jprot.2011.09.024] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 09/21/2011] [Accepted: 09/25/2011] [Indexed: 12/19/2022]
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69
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Yu LR. Pharmacoproteomics and toxicoproteomics: The field of dreams. J Proteomics 2011; 74:2549-53. [DOI: 10.1016/j.jprot.2011.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 10/03/2011] [Indexed: 01/09/2023]
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70
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Cho YE, Singh TSK, Lee HC, Moon PG, Lee JE, Lee MH, Choi EC, Chen YJ, Kim SH, Baek MC. In-depth identification of pathways related to cisplatin-induced hepatotoxicity through an integrative method based on an informatics-assisted label-free protein quantitation and microarray gene expression approach. Mol Cell Proteomics 2011; 11:M111.010884. [PMID: 22023808 DOI: 10.1074/mcp.m111.010884] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Cisplatin is used widely for treatment of a variety of cancer diseases. Recently, however, the use of cisplatin is restricted because of its adverse effects such as hepatotoxicity. There is no study with current proteomics technology to evaluate cisplatin-induced hepatotoxicity, even if some studies have reported on the hepatotoxicity. In this study, proteomic as well as genomic analyses have been used for identification of proteins and genes that respond to cisplatin treatment in rat primary hepatocytes. To investigate the hepatotoxic effects of cisplatin, rat primary hepatocytes were treated with an IC(20) concentration for 24 h. From proteomic analysis based on label-free quantitation strategy, cisplatin induced 76 up-regulated and 19 down-regulated proteins among 325 distinct proteins. In the mRNA level, genomic analysis revealed 72 up-regulated and 385 down-regulated genes in the cisplatin-treated group. Based on these two analyses, 19 pathways were commonly altered, whereas seven pathways were identified only by proteomic analysis, and 19 pathways were identified only by genomic analysis. Overall, this study explained the mechanism of cisplatin-induced hepatotoxicity with two points of view: well known pathways including drug metabolism, fatty acid metabolism, and glycolysis/TCA cycle and little known pathways including urea cycle and inflammation metabolism, for hepatotoxicity of other toxic agents. Up-regulated proteins detected by proteomic analysis in the cisplatin-treated group: FBP1 (fructose 1,6-bisphosphatase 1), FASN (fatty acid synthase), CAT (catalase), PRDX1 (peroxiredoxin-1), HSPD1 (60-kDa heat shock protein), MDH2 (malate dehydrogenase 2), and ARG1 (arginase 1), and also down-regulated proteins in the cisplatin-treated group: TPM1 (tropomyosin 1), TPM3 (tropomyosin 3), and CTSB (cathepsin B), were confirmed by Western blot analysis. In addition, up-regulated mRNAs detected by microarray analysis in the cisplatin-treated group: GSTA2, GSTT2, YC2, TXNRD1, CYP2E1, CYP2C13, CYP2D1, ALDH17, ARG1, ARG2, and IL-6, and also down-regulated mRNAs: CYP2C12, CYP26B1, TPM1, and TPM3, were confirmed by RT-PCR analysis. In case of PRDX1, FASN, and ARG1, they were further confirmed by immunofluorescence analysis. Through the integrated proteomic and genomic approaches, the present study provides the first pathway map related to cisplatin-induced hepatotoxicity, which may provide new insight into the mechanism of hepatotoxicity.
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Affiliation(s)
- Young-Eun Cho
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Thoudam S K Singh
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Hyun-Chul Lee
- D & P Biotech, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Pyong-Gon Moon
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Jeong-Eun Lee
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Myung-Hoon Lee
- D & P Biotech, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Eung-Chil Choi
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Sang-Hyun Kim
- Department of Pharmacology, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - Moon-Chang Baek
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea.
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71
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George J, Srivastava AK, Singh R, Shukla Y. Retracted: Cypermethrin exposure leads to regulation of proteins expression involved in neoplastic transformation in mouse skin. Proteomics 2011; 11:4411-21. [DOI: 10.1002/pmic.201100233] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 08/04/2011] [Accepted: 08/28/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Jasmine George
- Proteomics Laboratory, CSIR‐Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Amit Kumar Srivastava
- Proteomics Laboratory, CSIR‐Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Richa Singh
- Proteomics Laboratory, CSIR‐Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
| | - Yogeshwer Shukla
- Proteomics Laboratory, CSIR‐Indian Institute of Toxicology Research, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, India
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72
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Huang QY, Huang HQ. Differential expression profile of membrane proteins in zebrafish (Danio rerio
) brain exposed to methyl parathion. Proteomics 2011; 11:3743-56. [DOI: 10.1002/pmic.201100084] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 12/12/2022]
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73
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Buhrke T, Lengler I, Lampen A. Analysis of proteomic changes induced upon cellular differentiation of the human intestinal cell line Caco-2. Dev Growth Differ 2011; 53:411-26. [PMID: 21492153 DOI: 10.1111/j.1440-169x.2011.01258.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The human intestinal cell line Caco-2 is a well-established model system to study cellular differentiation of human enterocytes of intestinal origin, because these cells have the capability to differentiate spontaneously into polarized cells with morphological and biochemical features of small intestinal enterocytes. Therefore, the cells are widely used as an in vitro model for the human intestinal barrier. In this study, a proteomic approach was used to identify the molecular marker of intestinal cellular differentiation. The proteome of proliferating Caco-2 cells was compared with that of fully differentiated cells. Two-dimensional gel analysis yielded 53 proteins that were differently regulated during the differentiation process. Pathway analysis conducted with those 34 proteins that were identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) analysis revealed subsets of proteins with common molecular and cellular function. It was shown that proteins involved in xenobiotic and drug metabolism as well as in lipid metabolism were upregulated upon cellular differentiation. In parallel, proteins associated with proliferation, cell growth and cancer were downregulated, reflecting the loss of the tumorigenic phenotype of the cells. Thus, the proteomic approach in combination with a literature-based pathway analysis yielded valuable information about the differentiation process of Caco-2 cells on the molecular level that contributes to the understanding of the development of colon cancer or inflammatory diseases such as ulcerative colitis--diseases associated with an imbalanced differentiation process of intestinal cells.
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Affiliation(s)
- Thorsten Buhrke
- Food Safety Department, Federal Institute for Risk Assessment, Thielallee 88-92, 14195 Berlin, Germany.
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74
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Krewski D, Westphal M, Al-Zoughool M, Croteau MC, Andersen ME. New Directions in Toxicity Testing. Annu Rev Public Health 2011; 32:161-78. [DOI: 10.1146/annurev-publhealth-031210-101153] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Krewski
- McLaughlin Center for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5; , , ,
| | - Margit Westphal
- McLaughlin Center for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5; , , ,
| | - Mustafa Al-Zoughool
- McLaughlin Center for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5; , , ,
| | - Maxine C. Croteau
- McLaughlin Center for Population Health Risk Assessment, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5; , , ,
| | - Melvin E. Andersen
- Program in Chemical Safety Sciences, Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina 27709, USA;
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75
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Tyagi S, George J, Singh R, Bhui K, Shukla Y. Neoplastic Alterations Induced in Mammalian Skin Following Mancozeb Exposure Using In Vivo and In Vitro Models. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:155-67. [DOI: 10.1089/omi.2010.0076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Shilpa Tyagi
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), Lucknow 226001 (U.P), India
| | - Jasmine George
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), Lucknow 226001 (U.P), India
| | - Richa Singh
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), Lucknow 226001 (U.P), India
| | - Kulpreet Bhui
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), Lucknow 226001 (U.P), India
| | - Yogeshwer Shukla
- Proteomics Laboratory, Indian Institute of Toxicology Research, Council of Scientific & Industrial Research (CSIR), Lucknow 226001 (U.P), India
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76
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Sanchez BC, Ralston-Hooper K, Sepúlveda MS. Review of recent proteomic applications in aquatic toxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:274-282. [PMID: 21072841 DOI: 10.1002/etc.402] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates.
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77
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Léonard JF, Courcol M, Gautier JC. Optimization of SELDI for biomarker detection in plasma. Methods Mol Biol 2011; 691:351-68. [PMID: 20972765 DOI: 10.1007/978-1-60761-849-2_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The surface-enhanced laser desorption ionization (SELDI) technology is a promising approach not only for the research of biomarkers in the blood of patients in clinical applications but also in preclinical studies to assess the drug-induced toxicities. The optimization of the SELDI platform is a crucial step before running plasma samples from preclinical toxicity studies. First, mass spectrometer parameters such as the laser energy and ion focus mass values should be assessed in order to obtain the highest quality of spectra. Second, the coefficient of variation of the intensity, resolution, and signal-to-noise ratio of the peaks detected in reference samples should be evaluated and used as quality control criteria. Last, a systematic evaluation of technical bias such as the spot and chip position and the bioprocessor sequence number may be achieved using the appropriate multivariate statistical analyses.
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Affiliation(s)
- Jean-Francois Léonard
- Disposition, Safety and Animal Research, sanofi-aventis R&D, Vitry-sur-Seine, France.
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78
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Huang QY, Huang L, Huang HQ. Proteomic analysis of methyl parathion-responsive proteins in zebrafish (Danio rerio) brain. Comp Biochem Physiol C Toxicol Pharmacol 2011; 153:67-74. [PMID: 20826231 DOI: 10.1016/j.cbpc.2010.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/30/2010] [Accepted: 08/30/2010] [Indexed: 12/22/2022]
Abstract
Methyl parathion (MP), an organophosphorus pesticide used worldwide, has been associated with a wide spectrum of toxic effects on organisms in the environment. This study set out to analyze the alteration of protein profiles in MP-exposed zebrafish (Danio rerio) brain and find the proteins responsive to MP toxicity. Zebrafish were subjected to 1, 3 and 5mg/L MP and the proteomic changes in their brains were revealed using two-dimensional gel electrophoresis. Six protein spots were observed to be significantly changed by MP exposure. Among these, 4 spots were down-regulated, while 2 spots were up-regulated. These altered spots were excised from the gels and identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry and database searching. The results indicate that these proteins were involved in binding, catalysis, regulation of energy metabolism and cell structure. These data may provide novel biomarkers for the evaluation of MP contamination and useful insights for understanding the mechanisms of MP toxicity.
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Affiliation(s)
- Qing-Yu Huang
- Department of Biochemistry and Biotechnology, School of Life Sciences, Xiamen University, Xiamen 361005, China
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79
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Mörbt N, Tomm J, Feltens R, Mögel I, Kalkhof S, Murugesan K, Wirth H, Vogt C, Binder H, Lehmann I, von Bergen M. Chlorinated benzenes cause concomitantly oxidative stress and induction of apoptotic markers in lung epithelial cells (A549) at nonacute toxic concentrations. J Proteome Res 2010; 10:363-78. [PMID: 21171652 DOI: 10.1021/pr1005718] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In industrialized countries, people spend more time indoors and are therefore increasingly exposed to volatile organic compounds that are emitted at working places and from consumer products, paintings, and furniture, with chlorobenzene (CB) and 1,2-dichlorobenzene (DCB) being representatives of the halogenated arenes. To unravel the molecular effects of low concentrations typical for indoor and occupational exposure, we exposed human lung epithelial cells to CB and DCB and analyzed the effects on the proteome level by 2-D DIGE, where 860 protein spots were detected. A set of 25 and 30 proteins were found to be significantly altered due to exposure to environmentally relevant concentrations of 10(-2) g/m(3) of CB or 10(-3) g/m(3) of DCB (2.2 and 0.17 ppm), respectively. The most enriched pathways were cell death signaling, oxidative stress response, protein quality control, and metabolism. The involvement of oxidative stress was validated by ROS measurement. Among the regulated proteins, 28, for example, voltage-dependent anion-selective channel protein 2, PDCD6IP protein, heat shock protein beta-1, proliferating cell nuclear antigen, nucleophosmin, seryl-tRNA synthetase, prohibitin, and protein arginine N-methyltransferase 1, could be correlated with the molecular pathway of cell death signaling. Caspase 3 activation by cleavage was confirmed for both CB and DCB by immunoblotting. Treatment with CB or DCB also caused differential protein phosphorylation, for example, at the proteins HNRNP C1/C2, serine-threonine receptor associated protein, and transaldolase 1. Compared to previous results, where cells were exposed to styrene, for the chlorinated aromatic substances besides oxidative stress, apoptosis was found as the predominant cellular response mechanism.
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Affiliation(s)
- Nora Mörbt
- Department of Proteomics, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
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80
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Hepatic transcriptome and proteome responses against diethyl maleate-induced glutathione depletion in the rat. Arch Toxicol 2010; 85:1045-56. [DOI: 10.1007/s00204-010-0632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/24/2010] [Indexed: 10/18/2022]
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81
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Szopinska A, Morsomme P. Quantitative Proteomic Approaches and Their Application in the Study of Yeast Stress Responses. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2010; 14:639-49. [DOI: 10.1089/omi.2010.0045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Aleksandra Szopinska
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud Louvain-la-Neuve, Belgium
| | - Pierre Morsomme
- Université catholique de Louvain, Institut des Sciences de la Vie, Croix du Sud Louvain-la-Neuve, Belgium
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82
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Muñoz B, Albores A. The role of molecular biology in the biomonitoring of human exposure to chemicals. Int J Mol Sci 2010; 11:4511-25. [PMID: 21151453 PMCID: PMC3000097 DOI: 10.3390/ijms11114511] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 10/12/2010] [Accepted: 10/29/2010] [Indexed: 11/16/2022] Open
Abstract
Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues; results were used to evaluate potential health risk. However, this approach only estimates the presence of a noxious chemical and its effects, but does not prevent or diminish the risk. Molecular biology methods have become very useful in occupational medicine to provide more accurate and opportune diagnostics. In this review, we discuss the role of the following common techniques: (1) Use of cell cultures; (2) evaluation of gene expression; (3) the “omic” sciences (genomics, transcriptomics, proteomics and metabolomics) and (4) bioinformatics. We suggest that molecular biology has many applications in occupational health where the data can be applied to general environmental conditions.
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Affiliation(s)
- Balam Muñoz
- Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del IPN, Av. IPN 2508, México, DF 07360, Mexico; E-Mail:
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83
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Collins BC, Lau TYK, Pennington SR, Gallagher WM. Differential proteomics incorporating iTRAQ labeling and multi-dimensional separations. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2010; 691:369-83. [PMID: 20972766 DOI: 10.1007/978-1-60761-849-2_23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Considerable effort is currently being expended to integrate newly developed "omics"-based approaches (proteomics, transcriptomics, and metabonomics) into preclinical safety evaluation workflows in the hope that more sensitive prediction of toxicology can be achieved as reported by Waters and Fostel (Nat. Rev. Genet. 5(12):936-948, 2004) and Craig et al. (J. Proteome Res. 5(7):1586-1601, 2006). Proteomic approaches are well placed to contribute to this effort as (a) proteins are the metabolically active products of genes and, as such, may provide more sensitive and direct predictive information on drug-induced liabilities and (b) they have the potential to determine tissue leakage markers in peripheral fluids. Here, we describe a workflow for proteomic semi-quantitative expression profiling of liver from rats treated with a known hepatotoxicant using a multiplexed isobaric labeling strategy and multi-dimensional liquid chromatography.
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Affiliation(s)
- Ben C Collins
- UCD School of Biomolecular and Biomedical Science and Proteome Research Centre, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
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84
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Choi S, Park SY, Jeong J, Cho E, Phark S, Lee M, Kwak D, Lim JY, Jung WW, Sul D. Identification of toxicological biomarkers of di(2-ethylhexyl) phthalate in proteins secreted by HepG2 cells using proteomic analysis. Proteomics 2010; 10:1831-46. [PMID: 20198640 DOI: 10.1002/pmic.200900674] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effects of di(2-ethylhexyl) phthalate (DEHP) on proteins secreted by HepG2 cells were studied using a proteomic approach. HepG2 cells were exposed to various concentrations of DEHP (0, 2.5, 5, 10, 25, 50, 100, and 250 microM) for 24 or 48 h. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and comet assays were then conducted to determine the cytotoxicity and genotoxicity of DEHP, respectively. The MTT assay showed that 10 microM DEHP was the maximum concentration that did not cause cell death. In addition, the DNA damage in HepG2 cells exposed to DEHP was found to increase in a dose- and time-dependent fashion. Proteomic analysis using two different pI ranges (4-7 and 6-9) and large size 2-DE revealed the presence of 2776 protein spots. A total of 35 (19 up- and 16 down-regulated) proteins were identified as biomarkers of DEHP by ESI-MS/MS. Several differentiated protein groups were also found. Proteins involved in apoptosis, transportation, signaling, energy metabolism, and cell structure and motility were found to be up- or down-regulated. Among these, the identities of cystatin C, Rho GDP inhibitor, retinol binding protein 4, gelsolin, DEK protein, Raf kinase inhibitory protein, triose phosphate isomerase, cofilin-1, and haptoglobin-related protein were confirmed by Western blot assay. Therefore, these proteins could be used as potential biomarkers of DEHP and human disease associated with DEHP.
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Affiliation(s)
- Seonyoung Choi
- Graduate School of Medicine, Korea University, Sungbuk-Ku, Seoul, Republic of Korea
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85
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Identification of differential hepatic proteins in rare minnow (Gobiocypris rarus) exposed to pentachlorophenol (PCP) by proteomic analysis. Toxicol Lett 2010; 199:69-79. [PMID: 20732397 DOI: 10.1016/j.toxlet.2010.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 08/11/2010] [Accepted: 08/13/2010] [Indexed: 11/23/2022]
Abstract
Pentachlorophenol (PCP) is a ubiquitous contaminant that has been shown to lead to hepatoxicity and is implicated in the incidence of liver tumors in human. A number of previous studies have described the toxic effects of PCP based on conventional toxicological indices. However, little evidence on protein levels is available at present. For further understanding of mechanisms of action and identifying the potential protein biomarkers for PCP exposure, two-dimensional electrophoresis coupled with mass spectrometry has been used to identify proteins differentially expressed in the livers of rare minnow (Gobiocypris rarus) following PCP exposure of 0.5, 5, 50 μg/L. After comparison of the protein profiles from treated and control groups, 39 protein spots were found altered in abundance (>2-fold) from male and female PCP-treated groups. Matrix-assisted laser desorption/ionization (MALDI) tandem time-of-flight mass spectrometry (TOF/MS) analysis allowed the unambiguous identification, and 18 protein spots were identified successfully, 12 proteins in females and 6 proteins in males, respectively. These proteins were involved in transport, metabolism, response to oxidative stress and other biological processes. Of these proteins, four differentially expressed mRNA encoding proteins underwent quantitative analysis by quantitative real-time PCR (QRT-PCR). The consistent and discrepant results between mRNA and protein levels suggested that complicated regulatory mechanisms of gene expression were implicated in the response to PCP exposure. In addition, marked gender differences in response to PCP have been described from the comparison of the male and female liver protein profiles.
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86
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Collins BC, Sposny A, McCarthy D, Brandenburg A, Woodbury R, Pennington SR, Gautier JC, Hewitt P, Gallagher WM. Use of SELDI MS to discover and identify potential biomarkers of toxicity in InnoMed PredTox: a multi-site, multi-compound study. Proteomics 2010; 10:1592-608. [PMID: 20162557 DOI: 10.1002/pmic.200900608] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A serious bottleneck in the drug development pipeline is the inability of current pre-clinical toxicology evaluation methods to predict early on, and with good accuracy, that a drug candidate will have to be removed from development due to toxicology/safety issues. The InnoMed PredTox consortium attempted to address this issue by assessing the value of using molecular profiling techniques (proteomics, transcriptomics, and metabonomics), in combination with conventional toxicology measurements, on decision making earlier in pre-clinical safety evaluation. In this study, we report on the SELDI-TOF-MS proteomics component of the InnoMed PredTox project. In this large scale, multi-site, multi-compound study, tissue and plasma samples from 14-day in vivo rat experiments conducted for 16 hepato- and nephro-toxicants with known toxicology endpoints (including 14 proprietary compounds and 2 reference compounds) were analyzed by SELDI-TOF-MS. We have identified seven plasma proteins and four liver proteins which were shown to be modulated by treatment, and correlated with histopathological evaluations and can be considered potential biomarker candidates for the given toxicology endpoints. In addition, we report on the intra- and inter-site variations observed based on measurements from a reference sample, and steps that can be taken to minimize this variation.
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Affiliation(s)
- Ben C Collins
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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87
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Feingold BJ, Vegosen L, Davis M, Leibler J, Peterson A, Silbergeld EK. A niche for infectious disease in environmental health: rethinking the toxicological paradigm. ENVIRONMENTAL HEALTH PERSPECTIVES 2010; 118:1165-72. [PMID: 20385515 PMCID: PMC2920090 DOI: 10.1289/ehp.0901866] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 04/12/2010] [Indexed: 05/21/2023]
Abstract
OBJECTIVE In this review we highlight the need to expand the scope of environmental health research, which now focuses largely on the study of toxicants, to incorporate infectious agents. We provide evidence that environmental health research would be strengthened through finding common ground with the tools and approaches of infectious disease research. DATA SOURCES AND EXTRACTION We conducted a literature review for examples of interactions between toxic agents and infectious diseases, as well as the role of these interactions as risk factors in classic "environmental" diseases. We investigated existing funding sources and research mandates in the United States from the National Science Foundation and the National Institutes of Health, particularly the National Institute of Environmental Health Sciences. DATA SYNTHESIS We adapted the toxicological paradigm to guide reintegration of infectious disease into environmental health research and to identify common ground between these two fields as well as opportunities for improving public health through interdisciplinary research. CONCLUSIONS Environmental health encompasses complex disease processes, many of which involve interactions among multiple risk factors, including toxicant exposures, pathogens, and susceptibility. Funding and program mandates for environmental health studies should be expanded to include pathogens in order to capture the true scope of these overlapping risks, thus creating more effective research investments with greater relevance to the complexity of real-world exposures and multifactorial health outcomes. We propose a new model that integrates the toxicology and infectious disease paradigms to facilitate improved collaboration and communication by providing a framework for interdisciplinary research. Pathogens should be part of environmental health research planning and funding allocation, as well as applications such as surveillance and policy development.
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Affiliation(s)
- Beth J Feingold
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
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88
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89
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George J, Prasad S, Mahmood Z, Shukla Y. Studies on glyphosate-induced carcinogenicity in mouse skin: a proteomic approach. J Proteomics 2010; 73:951-64. [PMID: 20045496 DOI: 10.1016/j.jprot.2009.12.008] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 12/14/2009] [Accepted: 12/15/2009] [Indexed: 11/17/2022]
Abstract
Glyphosate is a widely used broad spectrum herbicide, reported to induce various toxic effects in non-target species, but its carcinogenic potential is still unknown. Here we showed the carcinogenic effects of glyphosate using 2-stage mouse skin carcinogenesis model and proteomic analysis. Carcinogenicity study revealed that glyphosate has tumor promoting activity. Proteomic analysis using 2-dimensional gel electrophoresis and mass spectrometry showed that 22 spots were differentially expressed (>2 fold) on glyphosate, 7, 12-dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoyl-phorbol-13-acetate (TPA) application over untreated control. Among them, 9 proteins (translation elongation factor eEF-1 alpha chain, carbonic anhydrase III, annexin II, calcyclin, fab fragment anti-VEGF antibody, peroxiredoxin-2, superoxide dismutase [Cu-Zn], stefin A3, and calgranulin-B) were common and showed similar expression pattern in glyphosate and TPA-treated mouse skin. These proteins are known to be involved in several key processes like apoptosis and growth-inhibition, anti-oxidant responses, etc. The up-regulation of calcyclin, calgranulin-B and down-regulation of superoxide dismutase [Cu-Zn] was further confirmed by immunoblotting, indicating that these proteins can be good candidate biomarkers for skin carcinogenesis induced by glyphosate. Altogether, these results suggested that glyphosate has tumor promoting potential in skin carcinogenesis and its mechanism seems to be similar to TPA.
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Affiliation(s)
- Jasmine George
- Proteomics Laboratory, Indian Institute of Toxicology Research (CSIR), Mahatma Gandhi Marg, Lucknow 226001 UP, India
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90
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Lee YH, Lin Q, Boelsterli UA, Chung MCM. The Sod2 mutant mouse as a model for oxidative stress: a functional proteomics perspective. MASS SPECTROMETRY REVIEWS 2010; 29:179-196. [PMID: 19294730 DOI: 10.1002/mas.20226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Oxidative stress has been implicated in the pathogenesis of numerous human diseases and disorders, but the mechanistic basis often remains enigmatic. The Sod2 mutant mouse, which is sensitized to mitochondrial stress, is an ideal mutant model for studying the role of oxidative stress in a diverse range of complications arising from mitochondrial dysfunction and diminished antioxidant defense. To fully appreciate the widespread molecular consequences under increased oxidative stress, a systems approach utilizing proteomics is able to provide a global overview of the complex biological changes, which a targeted single biomolecular approach cannot address fully. This review focuses on the applications of mass spectrometry and functional proteomics in the Sod2 mouse. The combinatorial approach provides novel insights into the interplay of chemistry and biology, free radicals and proteins, thereby augmenting our understanding of how redox perturbations influence protein dynamics. Ultimately, this knowledge can lead to the development of free radical-targeted therapies.
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Affiliation(s)
- Yie Hou Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore 117597, Singapore
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91
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George J, Singh R, Mahmood Z, Shukla Y. Toxicoproteomics: New paradigms in toxicology research. Toxicol Mech Methods 2010; 20:415-23. [DOI: 10.3109/15376511003667842] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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92
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Shi Z, Zhang H, Ding L, Feng Y, Wang J, Dai J. Proteomic analysis for testis of rats chronically exposed to perfluorododecanoic acid. Toxicol Lett 2010; 192:179-88. [DOI: 10.1016/j.toxlet.2009.10.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 10/13/2009] [Accepted: 10/15/2009] [Indexed: 01/01/2023]
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93
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Andersen ME, Al-Zoughool M, Croteau M, Westphal M, Krewski D. The future of toxicity testing. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2010; 13:163-196. [PMID: 20574896 DOI: 10.1080/10937404.2010.483933] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In 2007, the U.S. National Research Council (NRC) released a report, "Toxicity Testing in the 21st Century: A Vision and a Strategy," that proposes a paradigm shift for toxicity testing of environmental agents. The vision is based on the notion that exposure to environmental agents leads to adverse health outcomes through the perturbation of toxicity pathways that are operative in humans. Implementation of the NRC vision will involve a fundamental change in the assessment of toxicity of environmental agents, moving away from adverse health outcomes observed in experimental animals to the identification of critical perturbations of toxicity pathways. Pathway perturbations will be identified using in vitro assays and quantified for dose response using methods in computational toxicology and other recent scientific advances in basic biology. Implementation of the NRC vision will require a major research effort, not unlike that required to successfully map the human genome, extending over 10 to 20 years, involving the broad scientific community to map important toxicity pathways operative in humans. This article provides an overview of the scientific tools and technologies that will form the core of the NRC vision for toxicity testing. Of particular importance will be the development of rapidly performed in vitro screening assays using human cells and cell lines or human tissue surrogates to efficiently identify environmental agents producing critical pathway perturbations. In addition to the overview of the NRC vision, this study documents the reaction by a number of stakeholder groups since 2007, including the scientific, risk assessment, regulatory, and animal welfare communities.
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Affiliation(s)
- Melvin E Andersen
- Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina, USA
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94
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Toxicogenomic analysis of N-nitrosomorpholine induced changes in rat liver: Comparison of genomic and proteomic responses and anchoring to histopathological parameters. Toxicol Appl Pharmacol 2009; 241:230-45. [DOI: 10.1016/j.taap.2009.08.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 08/18/2009] [Indexed: 01/26/2023]
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95
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Matsumoto H, Yakabe Y, Saito K, Sumida K, Sekijima M, Nakayama K, Miyaura H, Saito F, Otsuka M, Shirai T. Discrimination of carcinogens by hepatic transcript profiling in rats following 28-day administration. Cancer Inform 2009; 7:253-69. [PMID: 20011461 PMCID: PMC2791490 DOI: 10.4137/cin.s3229] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This study aimed at discriminating carcinogens on the basis of hepatic transcript profiling in the rats administrated with a variety of carcinogens and non-carcinogens. We conducted 28-day toxicity tests in male F344 rats with 47 carcinogens and 26 non-carcinogens, and then investigated periodically the hepatic gene expression profiles using custom microarrays. By hierarchical cluster analysis based on significantly altered genes, carcinogens were clustered into three major groups (Group 1 to 3). The formation of these groups was not affected by the gene sets used as well as the administration period, indicating that the grouping of carcinogens was universal independent of the conditions of both statistical analysis and toxicity testing. Seventeen carcinogens belonging to Group 1 were composed of mainly rat hepatocarcinogens, most of them being mutagenic ones. Group 2 was formed by three subgroups, which were composed of 23 carcinogens exhibiting distinct properties in terms of genotoxicity and target tissues, namely nonmutagenic hepatocarcinogens, and mutagenic and nonmutagenic carcinogens both of which are targeted to other tissues. Group 3 contained 6 carcinogens including 4 estrogenic substances, implying the group of estrogenic carcinogens. Gene network analyses revealed that the significantly altered genes in Group 1 included Bax, Tnfrsf6, Btg2, Mgmt and Abcb1b, suggesting that p53-mediated signaling pathway involved in early pathologic alterations associated with preceding mutagenic carcinogenesis. Thus, the common transcriptional signatures for each group might reflect the early molecular events of carcinogenesis and hence would enable us to identify the biomarker genes, and then to develop a new assay for carcinogenesis prediction.
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Affiliation(s)
- Hiroshi Matsumoto
- Chemical Assessment Center, Chemicals Evaluation and Research Institute, Japan (CERI), 1600, Shimo-Takano, Sugito-machi, Kitakatsushika-gun, Saitama 345-0043, Japan.
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96
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Witzmann FA, Richardson MR. Two-dimensional gels for toxicological drug discovery applications. Expert Opin Drug Metab Toxicol 2009; 2:103-11. [PMID: 16863472 DOI: 10.1517/17425255.2.1.103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Two-dimensional gel electrophoresis (2DGE) continues to be a useful approach to study protein expression. Although liquid chromatographic and mass spectrometric approaches that overcome some of the limitations and labour intensity of 2DGE are increasingly popular, this electrophoretic approach still has exceptional relevance in toxicology. Despite the technical challenges, pharmacologists/toxicologists continue to use gel-based proteomics to assess the biological and health effects of chemical treatment and exposure. This brief review addresses the use of 2DGE-based proteomics in drug development and toxicology, emphasising its unique strengths and weaknesses, and considers recent developments in this strategy that have evolved to directly confront the issues of dynamic range and reproducibility that have previously limited the overall use of 2D electrophoresis.
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Affiliation(s)
- Frank A Witzmann
- Indiana University School of Medicine, Department of Cellular & Integrative Physiology, Biotechnology & Research Training Center, Indianapolis, IN 46202, USA.
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97
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Malécot M, Mezhoud K, Marie A, Praseuth D, Puiseux-Dao S, Edery M. Proteomic study of the effects of microcystin-LR on organelle and membrane proteins in medaka fish liver. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2009; 94:153-161. [PMID: 19628287 DOI: 10.1016/j.aquatox.2009.06.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Revised: 06/16/2009] [Accepted: 06/19/2009] [Indexed: 05/28/2023]
Abstract
The microcystin-leucine-arginine toxin (MC-LR) is produced by cyanobacteria that sometimes bloom in water reservoirs. It targets the liver, thus posing potential health risks to human and animals. Microcystin inhibits the protein phosphatases PP1 and PP2A, leading to diverse cellular deregulation processes. A proteomic approach was applied to the medaka fish (Oryzias latipes) to obtain an overview of the effects of MC-LR on the liver. As membrane and organelle proteins are major structural and functional components of several cell signalling pathways, we decided to investigate here the membrane and organelle-enriched fractions from the livers of control and MC-LR treated medaka fish. Seventeen proteins were identified by proteomic analysis as being modulated in response to MC-LR treatment. This is the first time for eight of them to be reported as being involved in MC-LR effects: prohibitin, fumarylacetoacetase, protein disulfide isomerase A4 and A6, glucose regulated protein 78kDa, 40S ribosomal protein SA, cytochrome b5, and ATP synthase mitochondrial d subunit. These proteins are involved in protein maturation or in the response to oxidative stress highlighting the role of organelles in protein processing and the complex cooperation associated with oxidative stress.
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Affiliation(s)
- Mélodie Malécot
- CNRS, FRE 3206 Molécules de communication et adaptation des microorganismes, and MNHN, USM 505 Cyanobactéries, cyanotoxines et environnement, Département Régulations, développement et diversité moléculaire, Muséum national d'Histoire naturelle, Paris Cedex 05, France
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98
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Ge F, He QY. Genomic and proteomic approaches for predicting toxicity and adverse drug reactions. Expert Opin Drug Metab Toxicol 2009; 5:29-37. [PMID: 19236227 DOI: 10.1517/17425250802661895] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND In the toxicology field, it remains a major challenge to predict and understand drug toxicity and adverse drug reactions (ADRs) in man. OBJECTIVE Recent progress in genomics and proteomics technologies and their application in predicting drug toxicity and ADRs. METHODS The key genomic and proteomic approaches are outlined, their applications in predicting toxicity and ADRs are described and their future developments in this field are discussed. CONCLUSION These technologies, used to measure expression at the transcript and protein levels, each convey different information and have different technical capabilities that can complement each other. The fields of genomics and proteomics continue to develop rapidly and it is already evident that genomic and proteomic approaches have much to contribute to the early prediction of drug toxicity and ADRs.
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Affiliation(s)
- Feng Ge
- Jinan University, Institute of Life and Health Engineering, Guangzhou, China
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99
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Fabre N, Anglade I, Vericat JA. Application of toxicogenomic tools in the drug research and development process. Toxicol Lett 2009; 186:13-7. [PMID: 19373985 DOI: 10.1016/j.toxlet.2009.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The cost for the development of new active and safe drugs is higher than ever and continues to increase. At the same time, both the pharmaceutical industry and the Regulatory Authorities are, despite the increasing effort to develop safer drugs, concerned by the risk of unexpected side effects observed in the late steps of the development of new drugs, either in late clinical development or after marketing approval. Then, the early knowledge of any potential toxic effect of a new drug is a key issue to allow adequate decision making. This means that current approaches based on the determination of the No-Adverse-Effect-Level and the Human-Equivalent-Dose are far from being perfect, and fail mainly to detect toxic phenomena of low intensity and/or low frequency. To improve the predictability of the existing experimental models, Toxicogenomics could be included into the in vitro candidate-selection steps and/or during the regulatory preclinical (or clinical) studies. In this communication, the authors present an example of the use of Toxicogenomic data to support decision making when selecting a new candidate to regulatory development. The authors also present a second example of integration of Toxicogenomics with the animal regulatory studies within the preclinical development of a new drug.
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Affiliation(s)
- Nicolas Fabre
- NOSCIRA SA, Department of Preclinical Development, Spain.
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100
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Gao Y, Holland RD, Yu LR. Quantitative proteomics for drug toxicity. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:158-66. [DOI: 10.1093/bfgp/elp006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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