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Mahfouz H, Dahran N, Abdel-Rahman Mohamed A, Abd El-Hakim YM, Metwally MMM, Alqahtani LS, Abdelmawlla HA, Wahab HA, Shamlan G, Nassan MA, Gaber RA. Stabilization of glutathione redox dynamics and CYP2E1 by green synthesized Moringa oleifera-mediated zinc oxide nanoparticles against acrylamide induced hepatotoxicity in rat model: Morphometric and molecular perspectives. Food Chem Toxicol 2023; 176:113744. [PMID: 36965644 DOI: 10.1016/j.fct.2023.113744] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/11/2023] [Accepted: 03/22/2023] [Indexed: 03/27/2023]
Abstract
The terrible reality is that acrylamide (AA) is a common food contaminant found in a wide variety of commonly consumed foods. This research involves the advancement of a more dependable technique for the bio-fabrication of zinc oxide nanoparticles (ZNPs) through the green method using Moringa Oleifera extract (MO-ZNPs) as an efficient chelating agent for acrylamide (AA). The effects of AA on glutathione redox dynamics, liver function, lipid profile, and zinc residues in Sprague Dawley rats are investigated. Finally, the microarchitecture and immunohistochemical staining of Caspase-3 and CYP2E1 were determined in the liver tissue of rats. Four separate groups, including control, MO-ZNPs (10 mg/kg b.wt), AA (20 mg/kg b.wt), and AA + MO-ZNPs for 60 days. The results revealed a suppressed activity of glutathione redox enzymes (GSH, GPX,and GSR) on both molecular and biochemical levels. Also, AA caused elevated liver enzymes, hepatosomatic index, and immunohistochemical staining of caspase-3 and CYP2E1 expression. MO-ZNPs co-treatment, on the other hand, stabilized glutathione-related enzyme gene expression, normalized hepatocellular enzyme levels, and restored hepatic tissue microarchitectures. It could be assumed that MO-ZNPs is a promising hepatoprotective molecule for alleviating AA-induced hepatotoxicity. We witnessed changes in glutathione redox dynamics to be restorative. Glutathione and cytochrome P450 2E1 play crucial roles in AA detoxification, so maintaining a healthy glutathione redox cycle is necessary for disposing of AA toxicity.
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Affiliation(s)
- Hala Mahfouz
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Kafrelsheikh University, Egypt
| | - Naief Dahran
- Department of Anatomy, Faculty of Medicine, University of Jeddah, Jeddah, Saudi Arabia
| | | | | | - Mohamed M M Metwally
- Department of Pathology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, 44511, Egypt
| | - Leena S Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 23445, Saudi Arabia
| | - Hassan Abdelraheem Abdelmawlla
- Department of Anatomy, College of Medicine, Jouf University, Saudi Arabia; Anatomy and Embryology Department, College of Medicine, Beni-Suef University, Egypt
| | - Hazim A Wahab
- Histology Department, Faculty of Medicine, Menofiya University, Shebin El Kom, Egypt
| | - Ghalia Shamlan
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh, 11362, Saudi Arabia
| | - Mohamed A Nassan
- Department of Clinical Laboratory Sciences, Turabah University College, Taif University, PO Box 11099,Taif, 21944, Saudi Arabia.
| | - Rasha A Gaber
- Medical Biochemistry Department, Faculty of Medicine, Tanta University, Egypt
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KDR polymorphism (1192G/A, 1719A/T) and modulation of ARV drug-induced hepatotoxicity. Microb Pathog 2021; 161:105243. [PMID: 34656700 DOI: 10.1016/j.micpath.2021.105243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 01/16/2023]
Abstract
Kinase insert Domain containing Receptor (KDR)/Vascular Endothelial Growth Factor Receptor (VEGFR-2) participate in endothelial dysfunction, which can lead to chronic liver disease. KDR reflects naturally against the toxicants from the damaged liver cells. Association of KDR polymorphism has been reported with many diseases including liver disease, but its role has not been described in ARV induced hepatotoxicity. Hence, we examined the exonic regions KDR (1192G/A, 1719A/T) polymorphism from 165 HIV-infected individuals (34/165 had ARV induced hepatotoxicity, 131/165 were with no hepatotoxicity) and 160 normal uninfected individuals by PCR-RFLP. In univariate analysis, KDR 1719 TT genotype presented at greater frequency from all HIV positive individuals in contrast with normal uninfected individuals (7.87% vs. 4.4%, OR = 1.72, P = 0.38). Individuals with KDR 1719 TT genotype had a risk for increasing hepatotoxicity and its severity (OR = 1.91, P = 0.38). Individuals with haplotype AT had risk for increasing hepatotoxicity and its severity (OR = 1.60, P = 0.50; OR = 2.35, P = 0.27). Whereas haplotype AA was associated with reduced risk of developing hepatotoxicity (OR = 0.40, P = 0.04). Individuals with KDR 1719 TT genotype were at greater risk of advancement of HIV disease (OR = 2.31, P = 0.23). Individuals with KDR 1719 TT genotype had more vulnerability for developing hepatotoxicity among alcohol users (OR = 2.57, P = 0.23). Individuals with KDR 1719 TT genotype were at higher risk of developing hepatotoxicity and its severity among nevirapine and alcohol consumers (OR = 2.47, P = 0.24; OR = 5.42, P = 0.42). In multivariate analysis, hepatotoxicity patients taking ART inclusive of nevirapine was associated with the severity of hepatotoxicity (OR = 4.82, P = 0.002). In conclusion, KDR 1719 TT genotype and haplotype AT may have a risk for development of hepatotoxicity and its severity. Haplotype AA may have influence to reduce the risk of developing hepatotoxicity.
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Madeira C, Costa PM. Proteomics in systems toxicology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:55-91. [PMID: 34340774 DOI: 10.1016/bs.apcsb.2021.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins are the ultimate product of gene expression. As they hinge between gene transcription and phenotype, they offer a more realistic perspective of toxicopathic effects, responses and even susceptibility to insult than targeting genes and mRNAs while dodging some inter-individual variability that hinders measuring downstream endpoints like metabolites or enzyme activity. Toxicologists have long focused on proteins as biomarkers but the advent of proteomics shifted risk assessment from narrow single-endpoint analyses to whole-proteome screening, enabling deriving protein-centric adverse outcome pathways (AOPs), which are pivotal for the derivation of Systems Biology informally named Systems Toxicology. Especially if coupled pathology, the identification of molecular initiating events (MIEs) and AOPs allow predictive modeling of toxicological pathways, which now stands as the frontier for the next generation of toxicologists. Advances in mass spectrometry, bioinformatics, protein databases and top-down proteomics create new opportunities for mechanistic and effects-oriented research in all fields, from ecotoxicology to pharmacotoxicology.
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Affiliation(s)
- Carolina Madeira
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal
| | - Pedro M Costa
- UCIBIO-Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Caparica, Portugal.
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Singh H, Lata S, Choudhari R, Dhole TN. Prevalence of ABCC3-1767G/A polymorphism among patients with antiretroviral-associated hepatotoxicity. Mol Genet Genomic Med 2020; 8:e1124. [PMID: 32212330 PMCID: PMC7284032 DOI: 10.1002/mgg3.1124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022] Open
Abstract
Background Plasma concentrations of antiretrovirals (ARVs) regimens have considerably varied in individuals of human immunodeficiency virus (HIV) because of variations in the expression of drug‐metabolizing and transporter genes. Transporter genes play an important role in the disposition of drugs. Polymorphism in transporter gene (ABCC3) affects the MRP3 expression and varies the treatment outcome. Method We examined the polymorphism of ABCC3‐1767G/A gene in a total of 165 HIV patients (out of 165 HIV patients, 34 were with and 131 were without hepatotoxicity) and 156 healthy individuals using the polymerase chain reaction–restriction fragment length polymorphism method. Results In univariate analysis, we found a decreased prevalence of ABCC3 1767GA, 1767GA+AA genotypes, and 1767A allele in patients with hepatotoxicity as compared to patients without hepatotoxicity (23.5% vs. 28.2% and 23.5% vs. 30.53%; 11.76% vs. 16.41%), while a higher prevalence of 1767AA genotype was observed in HIV patients in comparison with healthy controls (2.3% vs. 1.3%, odds ratio [OR] = 1.71, 95% confidence interval [CI]: 0.23–15.03, p = .89). The frequency of ABCC3‐1767AA genotype was dispersed higher in individuals with early and advanced HIV disease stage in comparison with healthy controls (5.3% vs. 1.3%, OR = 4.73, p = .70; 8.9% vs. 1.3%, OR = 1.89, p = .91). A higher occurrence of ABCC3‐1767AA genotype was found in tobacco using HIV patients without hepatotoxicity compared with nonusers (4.7% vs. 1.1%, OR = 4.28, p = .52). The distribution of ABCC3‐1767GA genotype was higher in nevirapine receiving HIV patients irrespective of their hepatotoxicity status as compared to nonusers (30.4% vs. 9.1%, OR = 3.34, p = .22; 29.4% vs. 16.7%, OR = 1.69, p = .77). In multivariate analysis, HIV patients receiving nevirapine and with hepatotoxicity was found to have a significant risk for severity of hepatotoxicity (OR = 4.56, 95% CI: 1.60–12.99, p = .004). Conclusion ABCC3 1767G/A polymorphism was not significantly associated with susceptibility to ARV‐associated hepatotoxicity, although ABCC3 1767AA genotype designated a risk for acquisition of hepatotoxicity and advancement of the disease. Nevirapine usage emerged as an independent risk factor for hepatotoxicity severity.
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Affiliation(s)
- HariOm Singh
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Sonam Lata
- Department of Molecular Biology, National AIDS Research Institute, Pune, India
| | - Ranjana Choudhari
- Department of Clinical Epidemiology, National Institute of Occupational Health, Ahmedabad, India
| | - Tapan N Dhole
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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Zwicker P, Schultze N, Niehs S, Albrecht D, Methling K, Wurster M, Wachlin G, Lalk M, Lindequist U, Haertel B. Differential effects of Helenalin, an anti-inflammatory sesquiterpene lactone, on the proteome, metabolome and the oxidative stress response in several immune cell types. Toxicol In Vitro 2017; 40:45-54. [DOI: 10.1016/j.tiv.2016.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022]
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Riebeling C, Jungnickel H, Luch A, Haase A. Systems Biology to Support Nanomaterial Grouping. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 947:143-171. [PMID: 28168668 DOI: 10.1007/978-3-319-47754-1_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.
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Affiliation(s)
- Christian Riebeling
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Harald Jungnickel
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andreas Luch
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andrea Haase
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany.
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Zwicker P, Schultze N, Niehs S, Methling K, Wurster M, Albrecht D, Bernhardt J, Wachlin G, Lalk M, Lindequist U, Haertel B. A proteomic approach for the identification of immunotoxic properties of Tulipalin A. Proteomics 2016; 16:2997-3008. [DOI: 10.1002/pmic.201600130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 01/13/2023]
Affiliation(s)
- Paula Zwicker
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Nadin Schultze
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Sarah Niehs
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Karen Methling
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Martina Wurster
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Dirk Albrecht
- Institute of Microbiology, Microbial Physiology and Molecular Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Microbial Physiology and Molecular Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Gerhild Wachlin
- Institute of Microbiology, Microbial Physiology and Molecular Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Michael Lalk
- Institute of Biochemistry, Biochemistry of Metabolism/Metabolomics; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Ulrike Lindequist
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
| | - Beate Haertel
- Institute of Pharmacy, Pharmaceutical Biology; Ernst-Moritz-Arndt-University; Greifswald Germany
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Suman S, Mishra S, Shukla Y. Toxicoproteomics in human health and disease: an update. Expert Rev Proteomics 2016; 13:1073-1089. [DOI: 10.1080/14789450.2016.1252676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shankar Suman
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Lucknow, India
| | - Sanjay Mishra
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Lucknow, India
| | - Yogeshwer Shukla
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Lucknow, India
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Nath Roy D, Goswami R, Pal A. Nanomaterial and toxicity: what can proteomics tell us about the nanotoxicology? Xenobiotica 2016; 47:632-643. [PMID: 27414072 DOI: 10.1080/00498254.2016.1205762] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
1. In the last few years, a substantial scientific work is focused to identify the potential toxicity of nanomaterials by studying the cellular pathways under in vitro and in vivo conditions. Owing to high surface area to volume ratio nanoparticles (NPs) can pass through cell membranes which might be responsible for creating adverse interactions in biological systems. Simultaneously, researchers are also interested to assess the fate of NP inside the living system, which may lead to altered protein expression as well as protein corona formation. 2. According to published reports, NP-mediated toxicity involves altered cellular system including cell morphology, cell differentiation, cell metabolism, cell mobility, cellular immunity, which is derived from the side effects of nanoformulation and leading to apoptosis and necrosis. These results indicate the existence of potential toxic effect of these particles to human health. 3. The advent of proteomics with sophisticated technical improvement coupled with advanced bioinformatics has led to identify altered proteins due to nanomaterial exposure that could provide a new avenue to biomarker discovery. 4. This review aims to provide the current status of safe production and use of nanomaterials.
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Affiliation(s)
- Dijendra Nath Roy
- a Department of Bioengineering , National Institute of Technology , Agartala , Tripura , India
| | - Ritobrata Goswami
- b Division of Biological & Life Sciences , School of Arts & Sciences, Ahmedabad University , Ahmedabad , Gujarat , India , and
| | - Ayantika Pal
- c Department of Human Physiology , Tripura University , Suryamaninagar , Tripura , India
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10
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Huang YC, Yu HS, Chai CY. Proteins in the ERK pathway are affected by arsenic-treated cells. Toxicol Res (Camb) 2015. [DOI: 10.1039/c4tx00218k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study revealed that arsenic regulates SLC25A12, PSME3, vinculin, QR and STIP1 expressions through activation of the ERK-signaling pathway.
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Affiliation(s)
- Ya-Chun Huang
- Department of Pathology
- College of Medicine
- Kaohsiung Medical University
- Kaohsiung City
- Taiwan
| | - Hsin-Su Yu
- Department of Dermatology
- College of Medicine
- Kaohsiung Medical University
- Kaohsiung City
- Taiwan
| | - Chee-Yin Chai
- Department of Pathology
- College of Medicine
- Kaohsiung Medical University
- Kaohsiung City
- Taiwan
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Lari P, Rashedinia M, Abnous K, Hosseinzadeh H. Alteration of protein profile in rat liver of animals exposed to subacute diazinon: A proteomic approach. Electrophoresis 2014; 35:1419-27. [DOI: 10.1002/elps.201300475] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 02/06/2023]
Affiliation(s)
- Parisa Lari
- Department of Pharmacodynamy and Toxicology; School of Pharmacy; Mashhad University of Medical Sciences; Mashhad Iran
| | - Marzieh Rashedinia
- Department of Pharmacodynamy and Toxicology; School of Pharmacy; Mashhad University of Medical Sciences; Mashhad Iran
| | - Khalil Abnous
- Department of Pharmacodynamy and Toxicology; School of Pharmacy; Mashhad University of Medical Sciences; Mashhad Iran
| | - Hossein Hosseinzadeh
- Department of Pharmacodynamy and Toxicology; School of Pharmacy; Mashhad University of Medical Sciences; Mashhad Iran
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Abstract
The emerging field of chemo- and pharmacoproteomics studies the mechanisms of action of bioactive molecules in a systems pharmacology context. In contrast to traditional drug discovery, pharmacoproteomics integrates the mechanism of a drug's action, its side effects including toxicity, and the discovery of new drug targets in a single approach. Thus, it determines early favorable (e.g. multiple kinase target in cancer drugs) and unfavorable (e.g. side effects) polypharmacology. Target profiling is accomplished using either active site-labeling probes or immobilized drugs. This strategy identifies direct targets and has in fact enabled even the determination of binding curves and half maximum inhibitory concentrations of these targets. In addition, the enrichment greatly reduces the complexity of the proteome to be analyzed by quantitative MS. Complementary to these approaches, global proteomics profiling studying drug treatement-induced changes in protein expression levels and/or post-translational modification status have started to become possible mostly due to significant improvements in instrumentation. Particularly, when using multidimensional separations, a considerable proteome depth of up to 10 000 proteins can be achieved with current state-of-the-art mass spectrometers and bioinformatics tools. In summary, chemo- and pharmacoproteomics has already contributed significantly to the identification of novel drug targets and their mechanisms of action(s). Aided by further technological advancements, this interdisciplinary approach will likely be used more broadly in the future.
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Affiliation(s)
- Sonja Hess
- Proteome Exploration Laboratory, Beckman Institute, California Institute of Technology, Pasadena, California 91125, USA.
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Qoronfleh MW. Role and challenges of proteomics in pharma and biotech: technical, scientific and commercial perspective. Expert Rev Proteomics 2014; 3:179-95. [PMID: 16608432 DOI: 10.1586/14789450.3.2.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Contemporary proteomics, currently in its exponential growth phase, is a bewildering array of tools. Proteomic methods are the result of a convergence of rapidly improving mass spectrometry technologies, protein chemistry and separation sciences, genomics and bioinformatics. Strides in improving proteomics technologies to map and measure proteomes and subproteomes are being made. However, no single proteomic platform appears ideally suited to address all research needs or accomplish ambitious goals satisfactorily. However, proteomics is in a unique position to contribute to protein discovery and to public health in terms of better biomarkers, diagnostics and treatment of disease. While the potential is great, many challenges and issues remain to be solved. Fundamental issues, such as biological variability, pre-analytic factors and analytical reproducibility, remain to be resolved. Neither an all-genetic approach nor an all-proteomic approach will solve biological complexity. Proteomics will be the foundation for constructing and extracting useful knowledge to pharma and biotech depicted in the following path: data --> structured data --> information --> information architecture --> knowledge --> useful knowledge.
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Affiliation(s)
- M Walid Qoronfleh
- Core Technology Alliance CTA, University of Michigan, Ann Arbor, MI 48109-1274, USA.
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14
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Verma N, Pink M, Rettenmeier AW, Schmitz-Spanke S. Benzo[a]pyrene-mediated toxicity in primary pig bladder epithelial cells: A proteomic approach. J Proteomics 2013; 85:53-64. [DOI: 10.1016/j.jprot.2013.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 03/21/2013] [Accepted: 04/09/2013] [Indexed: 02/03/2023]
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15
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Wang ZY, Kang H, Ji LL, Yang YQ, Liu TY, Cao ZW, Morahan G, Wang ZT. Proteomic characterization of the possible molecular targets of pyrrolizidine alkaloid isoline-induced hepatotoxicity. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2012; 34:608-617. [PMID: 22885678 DOI: 10.1016/j.etap.2012.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 06/12/2012] [Accepted: 06/23/2012] [Indexed: 06/01/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are distributed in plants worldwide including medicinal herbs or teas. In the present study, we investigated the effects of isoline, which is a retronecine-type PA isolated from traditional Chinese medicinal herb Ligularia duciformis, on mouse liver proteins by using proteomic approaches. Firstly, our results showed that 110mg/kg isoline increased alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities in serum, and hepatic tissue pathological observation further confirmed isoline-induced liver injury. Proteomic analysis showed that the liver samples from mice of isoline group demonstrated about 13 differentially expressed proteins compared with normal group, and those proteins may be involved in isoline-induced liver injury in mice. Next, all these 13 protein spots were identified by MALDI-TOF-TOF MS or LTQ MS; and among them 9 differentially expressed proteins are involved in the process of oxidative stress or cellular energy metabolism. Further lipid peroxidation analysis and ATPase assay confirmed the existing of oxidative injury induced by isoline and consequent disruption of energy metabolism. Furthermore, an in silico drug target searching program INVDOCK identified 2 potential protein targets of isoline, and the results are in support of proteomic analysis. In summary, the possible signaling molecules related with isoline-induced liver injury were demonstrated in this study.
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Affiliation(s)
- Zai-Yong Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201210, China; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai, 201210, China
| | - Hong Kang
- Department of Biomedical Engineering, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Li-Li Ji
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201210, China; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai, 201210, China.
| | - Yong-Qing Yang
- Shanghai Research Institute of Acupuncture and Meridian, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Tian-Yu Liu
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201210, China
| | - Zhi-Wei Cao
- Department of Biomedical Engineering, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Grant Morahan
- Western Australian Institute for Medical Research, the University of Western Australia, Perth WA 6000, Australia
| | - Zheng-Tao Wang
- The MOE Key Laboratory for Standardization of Chinese Medicines and The SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201210, China; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai, 201210, China.
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Verma N, Pink M, Rettenmeier AW, Schmitz-Spanke S. Review on proteomic analyses of benzo[a]pyrene toxicity. Proteomics 2012; 12:1731-55. [DOI: 10.1002/pmic.201100466] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Nisha Verma
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
| | - Mario Pink
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
| | - Albert W. Rettenmeier
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
| | - Simone Schmitz-Spanke
- Institute of Hygiene and Occupational Medicine; University Hospital Essen; Essen Germany
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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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18
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Ohyama K, Shiokawa A, Ito K, Masuyama R, Ichibangase T, Kishikawa N, Imai K, Kuroda N. Toxicoproteomic analysis of a mouse model of nonsteroidal anti-inflammatory drug-induced gastric ulcers. Biochem Biophys Res Commun 2012; 420:210-5. [PMID: 22426477 DOI: 10.1016/j.bbrc.2012.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Accepted: 03/02/2012] [Indexed: 12/11/2022]
Abstract
Nonsteroidal anti-inflammatory drugs (NSAIDs) are valuable agents; however, their use has been limited by their association with mucosal damage in the upper gastrointestinal tract. NSAIDs inhibit cyclooxygenase and consequently block the synthesis of prostaglandins, which have cytoprotective effects in gastric mucosa; these effects on prostaglandins have been thought to be major cause of NSAID-induced ulceration. However, studies indicate that additional NSAID-related mechanisms are involved in formation of gastric lesions. Here, we used a toxicoproteomic approach to understand cellular processes that are affected by NSAIDs in mouse stomach tissue during ulcer formation. We used fluorogenic derivatization-liquid chromatography-tandem mass spectrometry (FD-LC-MS/MS)-which consists of fluorogenic derivatization, separation and fluorescence detection by LC, and identification by LC-tandem mass spectrometry-in this proteomic analysis of pyrolic stomach from control and diclofenac (Dic)-treated mice. FD-LC-MS/MS results were highly sensitive; 10 differentially expressed proteins were identified, and all 10 were more highly expressed in Dic-treated mice than in control mice. Specifically, expression levels of 78 kDa glucose-regulated protein (GRP78), heat shock protein beta-1 (HSP27), and gastrin were more than 3-fold higher in Dic-treated mice than in control mice. This study represents a first step to ascertain the precise actors of early NSAID-induced ulceration.
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Affiliation(s)
- Kaname Ohyama
- Department of Environmental and Pharmaceutical Sciences, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
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19
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Lee YJ, Choi IK, Sheen YY, Park SN, Kwon HJ. Identification of EBP50 as a specific biomarker for carcinogens via the analysis of mouse lymphoma cellular proteome. Mol Cells 2012; 33:309-16. [PMID: 22434383 PMCID: PMC3887708 DOI: 10.1007/s10059-012-2280-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 12/30/2011] [Accepted: 01/11/2012] [Indexed: 11/30/2022] Open
Abstract
To identify specific biomarkers generated upon exposure of L5178Y mouse lymphoma cells to carcinogens, 2-DE and MALDI-TOF MS analysis were conducted using the cellular proteome of L5178Y cells that had been treated with the known carcinogens, 1,2-dibromoethane and O-nitrotoluene and the noncarcinogens, emodin and D-mannitol. Eight protein spots that showed a greater than 1.5-fold increase or decrease in intensity following carcinogen treatment compared with treatment with noncarcinogens were selected. Of the identified proteins, we focused on the candidate biomarker ERM-binding phosphoprotein 50 (EBP50), the expression of which was specifically increased in response to treatment with the carcinogens. The expression level of EBP50 was determined by western analysis using polyclonal rabbit anti-EBP50 antibody. Further, the expression level of EBP50 was increased in cells treated with seven additional carcinogens, verifying that EBP50 could serve as a specific biomarker for carcinogens.
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Affiliation(s)
- Yoen Jung Lee
- Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749,
Korea
| | - In-Kwon Choi
- Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749,
Korea
| | | | | | - Ho Jeong Kwon
- Department of Biotechnology, Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749,
Korea
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20
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Lee YJ, Choi IK, Sheen YY, Park SN, Kwon HJ. Moesin is a biomarker for the assessment of genotoxic carcinogens in mouse lymphoma. Mol Cells 2012; 33:203-10. [PMID: 22358511 PMCID: PMC3887720 DOI: 10.1007/s10059-012-2271-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Accepted: 12/07/2011] [Indexed: 10/28/2022] Open
Abstract
1,2-Dibromoethane and glycidol are well known genotoxic carcinogens, which have been widely used in industry. To identify a specific biomarker for these carcinogens in cells, the cellular proteome of L5178Y mouse lymphoma cells treated with these compounds was analyzed by 2-dimensional gel electrophoresis (2-DE) and MALDI-TOF mass spectrometry (MS). Of 50 protein spots showing a greater than 1.5-fold increase or decrease in intensity compared to control cells on a 2-D gel, we focused on the candidate biomarker moesin. Western analysis using monoclonal rabbit anti-moesin confirmed the identity of the protein and its increased level of expression upon exposure to the carcinogenic compounds. Moesin expression also increased in cells treated with six additional genotoxic carcinogens, verifying that moesin could serve as a biomarker to monitor phenotypic change upon exposure to genotoxic carcinogens in L5178Y mouse lymphoma cells.
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Affiliation(s)
- Yoen Jung Lee
- Department of Biotechnology, Yonsei University, Seoul 120-749,
Korea
- Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749,
Korea
| | - In-Kwon Choi
- Department of Biotechnology, Yonsei University, Seoul 120-749,
Korea
- Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749,
Korea
| | - Yhun Yhong Sheen
- College of Pharmacy, Ewha Womans University, Seoul 120-750,
Korea
| | - Sue Nie Park
- Hazardous Substances Analysis Division at Seoul Regional FDA, Korea Food and Drug Administration, Seoul 158-050,
Korea
| | - Ho Jeong Kwon
- Department of Biotechnology, Yonsei University, Seoul 120-749,
Korea
- Translational Research Center for Protein Function Control, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749,
Korea
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21
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Göransson Nyberg A, Stricklin D, Sellström Å. Mass casualties and health care following the release of toxic chemicals or radioactive material--contribution of modern biotechnology. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2011; 8:4521-49. [PMID: 22408587 PMCID: PMC3290976 DOI: 10.3390/ijerph8124521] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 11/16/2022]
Abstract
Catastrophic chemical or radiological events can cause thousands of casualties. Such disasters require triage procedures to identify the development of health consequences requiring medical intervention. Our objective is to analyze recent advancements in biotechnology for triage in mass emergency situations. In addition to identifying persons "at risk" of developing health problems, these technologies can aid in securing the unaffected or "worried well". We also highlight the need for public/private partnerships to engage in some of the underpinning sciences, such as patho-physiological mechanisms of chemical and radiological hazards, and for the necessary investment in the development of rapid assessment tools through identification of biochemical, molecular, and genetic biomarkers to predict health effects. For chemical agents, biomarkers of neurotoxicity, lung damage, and clinical and epidemiological databases are needed to assess acute and chronic effects of exposures. For radiological exposures, development of rapid, sensitive biomarkers using advanced biotechnologies are needed to sort exposed persons at risk of life-threatening effects from persons with long-term risk or no risk. The final implementation of rapid and portable diagnostics tools suitable for emergency care providers to guide triage and medical countermeasures use will need public support, since commercial incentives are lacking.
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Affiliation(s)
- Ann Göransson Nyberg
- Swedish Defence Research Agency, FOI CBRN—Defence and Security, 20 Cementvägen, SE 901 82 Umea, Sweden
| | - Daniela Stricklin
- Applied Research Associates, Inc., 1235 South Clark Street Ste, Arlington, VA 22203, USA;
| | - Åke Sellström
- European CBRNE Center, KBC Building, 6 Linnaeus väg, SE 901 87 Umea, Sweden;
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22
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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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23
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Cheng F, Theodorescu D, Schulman IG, Lee JK. In vitro transcriptomic prediction of hepatotoxicity for early drug discovery. J Theor Biol 2011; 290:27-36. [PMID: 21884709 DOI: 10.1016/j.jtbi.2011.08.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/27/2011] [Accepted: 08/11/2011] [Indexed: 01/08/2023]
Abstract
Liver toxicity (hepatotoxicity) is a critical issue in drug discovery and development. Standard preclinical evaluation of drug hepatotoxicity is generally performed using in vivo animal systems. However, only a small number of preselected compounds can be examined in vivo due to high experimental costs. A more efficient yet accurate screening technique that can identify potentially hepatotoxic compounds in the early stages of drug development would thus be valuable. Here, we develop and apply a novel genomic prediction technique for screening hepatotoxic compounds based on in vitro human liver cell tests. Using a training set of in vivo rodent experiments for drug hepatotoxicity evaluation, we discovered common biomarkers of drug-induced liver toxicity among six heterogeneous compounds. This gene set was further triaged to a subset of 32 genes that can be used as a multi-gene expression signature to predict hepatotoxicity. This multi-gene predictor was independently validated and showed consistently high prediction performance on five test sets of in vitro human liver cell and in vivo animal toxicity experiments. The predictor also demonstrated utility in evaluating different degrees of toxicity in response to drug concentrations, which may be useful not only for discerning a compound's general hepatotoxicity but also for determining its toxic concentration.
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Affiliation(s)
- Feng Cheng
- Department of Biophysics, University of Virginia, Charlottesville, VA, USA.
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24
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Genomic instability of gold nanoparticle treated human lung fibroblast cells. Biomaterials 2011; 32:5515-23. [DOI: 10.1016/j.biomaterials.2011.04.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 04/06/2011] [Indexed: 12/27/2022]
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25
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Jena G, Vikram A, Tripathi DN, Ramarao P. Use of chemoprotectants in chemotherapy and radiation therapy: the challenges of selecting an appropriate agent. Integr Cancer Ther 2011; 9:253-8. [PMID: 20702492 DOI: 10.1177/1534735410376633] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chemoprotection refers to the protection from the toxicity of one chemical by the intervention of another. Conflicting preclinical and clinical reports make it difficult to either ignore or accept the use of chemoprotectants during cancer chemotherapy or radiotherapy. The selection of anticancer drugs depends on the type and stage of cancer development. However, very little attention has been paid to the selection of chemoprotectants. The answer to the use of chemoprotectants during cancer therapy lies in their appropriate selection in a case-specific and/or issue-specific manner. The need of the hour is to find better answers on the rationality of chemoprotectants selection during cancer therapy using cutting-edge science. In this commentary, we have presented few examples to justify our view-points.
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Affiliation(s)
- Gopabandhu Jena
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Mohali, Punjab, India.
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26
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Alvergnas M, Rouleau A, Lucchi G, Heyd B, Ducoroy P, Richert L, Martin H. Proteomic mapping of bezafibrate-treated human hepatocytes in primary culture using two-dimensional liquid chromatography. Toxicol Lett 2011; 201:123-9. [DOI: 10.1016/j.toxlet.2010.12.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 12/17/2010] [Accepted: 12/21/2010] [Indexed: 10/25/2022]
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27
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Perez JD, Colucci JA, Sakata MM, Cunha TS, Arita DY, Casarini DE. Proteomic Approaches in Understanding a Detected Relationship between Chemotherapy-Induced Nephrotoxicity and Cell Respiration in HK-2 Cells. ACTA ACUST UNITED AC 2011; 119:p1-10. [DOI: 10.1159/000327575] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 03/09/2011] [Indexed: 11/19/2022]
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28
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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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29
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Ohyama K, Tomonari M, Ichibangase T, To H, Kishikawa N, Nakashima K, Imai K, Kuroda N. A toxicoproteomic study on cardioprotective effects of pre-administration of docetaxel in a mouse model of adriamycin-induced cardiotoxicity. Biochem Pharmacol 2010; 80:540-7. [DOI: 10.1016/j.bcp.2010.04.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 04/30/2010] [Accepted: 04/30/2010] [Indexed: 11/25/2022]
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30
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Leroy D, Haubruge E, De Pauw E, Thomé JP, Francis F. Development of ecotoxicoproteomics on the freshwater amphipod Gammarus pulex: identification of PCB biomarkers in glycolysis and glutamate pathways. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2010; 73:343-352. [PMID: 20015547 DOI: 10.1016/j.ecoenv.2009.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 11/17/2009] [Accepted: 11/18/2009] [Indexed: 05/28/2023]
Abstract
PCBs are persistent organic pollutants largely distributed in the biosphere. Although their effects on vertebrates are well described, little is known about their action on freshwater invertebrate's metabolism. Gammarus pulex (Linné) was selected as an indicator model to develop a proteomic approach in order to characterize the effects of PCBs on the protein profile of this freshwater crustacean. Sublethal coplanar PCBs exposition and related 2D gel were performed. More than 560 spots were detected and a total of 21 proteins exhibiting significant expression differences in PCB exposed to G. pulex were identified by mass spectrometry. Database searches were conducted to relate the results to well-known metabolic pathways (pentose phosphate, cytoskeleton, energy, etc.). In particular, glyceraldehyde 3-phosphate dehydrogenase and arginine kinase were found to be sensitive to the PCB exposition of G. pulex. The aim of the present study was to assess the biochemical responses and the metabolic changes in G. pulex following intoxication to coplanar PCB congeners CB77 and CB169 by a proteomic approach. This approach allowed us, by the identification of key proteins, to highlight important biochemical mechanisms disturbed by the presence of these contaminants in G. pulex.
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Affiliation(s)
- D Leroy
- Laboratory of Animal Ecology and Ecotoxicology, CART (Centre d'Analyse des Résidus en Traces), Liege University, Belgium.
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31
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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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32
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Cheng F, Cho SH, Lee JK. Multi-gene expression-based statistical approaches to predicting patients' clinical outcomes and responses. Methods Mol Biol 2010; 620:471-484. [PMID: 20652516 DOI: 10.1007/978-1-60761-580-4_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Gene expression profiling technique now enables scientists to obtain a genome-wide picture of cellular functions on various human disease mechanisms which has also proven to be extremely valuable in forecasting patients' prognosis and therapeutic responses. A wide range of multivariate techniques have been employed in biomedical applications on such expression profiling data in order to identify expression biomarkers that are highly associated with patients' clinical outcome and to train multi-gene prediction models that can forecast various human disease outcome and drug toxicities. We provide here a brief overview on some of these approaches, succinctly summarizing relevant basic concepts, statistical algorithms, and several practical applications. We also introduce our recent in vitro molecular expression-based algorithm, the so-called COXEN technique, which uses specialized gene profile signatures as a Rosetta Stone for translating the information between two different biological systems or populations.
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Affiliation(s)
- Feng Cheng
- Department of Biophysics, University of Virginia, Charlottesville, VA, USA
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33
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Merrick BA, Witzmann FA. The role of toxicoproteomics in assessing organ specific toxicity. EXS 2009; 99:367-400. [PMID: 19157068 DOI: 10.1007/978-3-7643-8336-7_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aims of this chapter on the role of toxicoproteomics in assessing organ-specific toxicity are to define the field of toxicoproteomics, describe its development among global technologies, and show potential uses in experimental toxicological research, preclinical testing and mechanistic biological research. Disciplines within proteomics deployed in preclinical research are described as Tier I analysis, involving global protein mapping and protein profiling for differential expression, and Tier II proteomic analysis, including global methods for description of function, structure, interactions and post-translational modification of proteins. Proteomic platforms used in toxicoproteomics research are briefly reviewed. Preclinical toxicoproteomic studies with model liver and kidney toxicants are critically assessed for their contributions toward understanding pathophysiology and in biomarker discovery. Toxicoproteomics research conducted in other organs and tissues are briefly discussed as well. The final section suggests several key developments involving new approaches and research focus areas for the field of toxicoproteomics as a new tool for toxicological pathology.
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Affiliation(s)
- B Alex Merrick
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, Durham, NC 27709, USA.
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34
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Merrick BA. Toxicoproteomics: Correlating Tissue and Serum Proteomics in Liver Injury. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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35
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Collins BC, Clarke A, Kitteringham NR, Gallagher WM, Pennington SR. Use of proteomics for the discovery of early markers of drug toxicity. Expert Opin Drug Metab Toxicol 2007; 3:689-704. [DOI: 10.1517/17425255.3.5.689] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Bermúdez-Crespo J, López JL. A better understanding of molecular mechanisms underlying human disease. Proteomics Clin Appl 2007; 1:983-1003. [PMID: 21136752 DOI: 10.1002/prca.200700086] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Indexed: 01/06/2023]
Abstract
This review summarises and discusses the degree to which proteomics is contributing to medical care, providing examples and signspots for future directions. Why do genomic approaches provide a limited view of gene expression? Because of the multifactorial nature of many diseases, proteomics enables us to understand the molecular basis of disease, not only at the organism, whole-cell or tissue levels, but also in subcellular structures, protein complexes and biological fluids. The application of proteomics in medicine is expected to have a major impact by providing an integrated view of individual disease processes. This review describes several proteomic platforms and examines the role of proteomics as a tool for clinical biomarker discovery, the identification of prognostic and earlier diagnostic markers, their use in monitoring the effects of drug treatments and eventually find more efficient and safer therapeutics for a wide range of pathologies.
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Affiliation(s)
- José Bermúdez-Crespo
- Department of Genetics, Faculty of Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
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37
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Yamanaka H, Yakabe Y, Saito K, Sekijima M, Shirai T. Quantitative proteomic analysis of rat liver for carcinogenicity prediction in a 28-day repeated dose study. Proteomics 2007; 7:781-95. [PMID: 17295351 DOI: 10.1002/pmic.200600235] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The potential of quantitative proteomic analysis to predict carcinogenicity of chemical compounds was investigated. Using 2D-DIGE, we analyzed the effects of 63 chemical compounds on protein expression in the rat liver after 28 daily doses. Types of carcinogens were categorized depending on the species and organ specificity. The carcinogen characteristic proteins for each classification were identified by Welch's t value. For evaluation of the predictive concordance we used support vector machines. The rat hepatic carcinogen-specific classification gave higher concordance than the other classification. The generalization performance was measured by leave-one-out cross-validation. For genotoxic and non-genotoxic compounds, a concordance of 79.3 and 76.5%, respectively, was obtained by the top 30 ranked proteins with Welch's t value. Furthermore, we found that the increase of the expression level of the stress response proteins as the common feature of poorly predicted chemical compounds in the leave-20%-out cross-validation. Quantitative proteomics could be promising technique for developing biomarker panels that can be used for carcinogenicity prediction. The list of proteins identified in this study and the zoomed gel images of the top ranked proteins in statistic analysis are provided in Supplementary Data.
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Affiliation(s)
- Hidenori Yamanaka
- Chemicals Assessment Center, Chemicals Evaluation and Research Institute, Saitama, Japan.
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38
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Yamamoto T, Tomizawa K, Fujikawa M, Sato Y, Yamada H, Horii I. EVALUATION OF HUMAN HEPATOCYTE CHIMERIC MICE AS A MODEL FOR TOXICOLOGICAL INVESTIGATION USING PANOMIC APPROACHES - EFFECT OF ACETAMINOPHEN ON THE EXPRESSION PROFILES OF PROTEINS AND ENDOGENOUS METABOLITES IN LIVER, PLASMA AND URINE. J Toxicol Sci 2007; 32:205-15. [PMID: 17785938 DOI: 10.2131/jts.32.205] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Toxicological responses to acetaminophen (APAP) overdose were evaluated in human hepatocytes transplanted chimeric mice using 2-dimensional gel electrophoresis (2DE)-based proteomics and (1)H-nuclear magnetic resonance (NMR)-based metabonomics. Huge variations, which were supported by histopathological findings, were observed in proteins expression in chimeric mice liver. The proteomic analysis of the livers showed that the proteins involved in the pathways of lipid/fatty acid metabolism, glycolysis and energy metabolism/production were affected. In addition, oxidative stress-related proteins showed altered expression. The metabonomic analysis of urine and plasma revealed alterations of endogenous metabolites, which were the intermediates involved in the tricarboxylic acid (TCA) cycle. Those findings were already confirmed in normal mice. We hypothesized that the mechanism of APAP-induced effects on chimeric mice liver was in accordance with the mechanism observed in normal mice. Therefore, these toxicopanomic approaches successfully revealed that the mechanisms in humans were identical with "known" APAP-induced hepatotoxicity detected in chimeric mice. Further investigations are needed to detect idiosyncratic hepatotoxicity in humans using chimeric mice.
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Affiliation(s)
- Toshinori Yamamoto
- Drug Safety Research & Development, Pfizer Global Research & Development, Nagoya Laboratories, Pfizer Inc., 5-2 Taketoyo, Aichi 470-2393, Japan.
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39
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Inadera H, Uchida M, Shimomura A. [Advances in "omics" technologies for toxicological research]. Nihon Eiseigaku Zasshi 2007; 62:18-31. [PMID: 17334089 DOI: 10.1265/jjh.62.18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Toxicology research can be applied to evaluate potential human health risks resulting from exposure to chemicals and other factors in the environment. The tremendous advances that have been made in high-throughput "omics" technologies (e.g., genomics, transcriptomics, proteomics and metabolomics) are providing good tools for toxicological research. Toxicogenomics is the study of changes in gene expression, protein and metabolite profiles, and combines the tools of traditional toxicology with those of genomics and bioinformatics. In particular, identification of changes in gene expression using DNA microarrays is an important method for understanding toxicological processes and obtaining an informative biomarker. Although these technologies have emerged as a powerful tool for clarifying hazard mechanisms, there are some concerns for the application of these technologies to toxicological research. This review summarizes the impact of "omics" technologies in toxicological study, followed by a brief discussion of future research.
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Affiliation(s)
- Hidekuni Inadera
- Department of Public Health, Faculty of Medicine, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
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Biron DG, Brun C, Lefevre T, Lebarbenchon C, Loxdale HD, Chevenet F, Brizard JP, Thomas F. The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 2006; 6:5577-96. [PMID: 16991202 DOI: 10.1002/pmic.200600223] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The elucidation of the entire genomic sequence of various organisms, from viruses to complex metazoans, most recently man, is undoubtedly the greatest triumph of molecular biology since the discovery of the DNA double helix. Over the past two decades, the focus of molecular biology has gradually moved from genomes to proteomes, the intention being to discover the functions of the genes themselves. The postgenomic era stimulated the development of new techniques (e.g. 2-DE and MS) and bioinformatics tools to identify the functions, reactions, interactions and location of the gene products in tissues and/or cells of living organisms. Both 2-DE and MS have been very successfully employed to identify proteins involved in biological phenomena (e.g. immunity, cancer, host-parasite interactions, etc.), although recently, several papers have emphasised the pitfalls of 2-DE experiments, especially in relation to experimental design, poor statistical treatment and the high rate of 'false positive' results with regard to protein identification. In the light of these perceived problems, we review the advantages and misuses of bioinformatics tools - from realisation of 2-DE gels to the identification of candidate protein spots - and suggest some useful avenues to improve the quality of 2-DE experiments. In addition, we present key steps which, in our view, need to be to taken into consideration during such analyses. Lastly, we present novel biological entities named 'interactomes', and the bioinformatics tools developed to analyse the large protein-protein interaction networks they form, along with several new perspectives of the field.
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Affiliation(s)
- David G Biron
- GEMI, UMR CNRS/IRD 2724, Centre IRD, Montpellier, France.
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Kroeger M. How omics technologies can contribute to the ‘3R’ principles by introducing new strategies in animal testing. Trends Biotechnol 2006; 24:343-6. [PMID: 16782220 DOI: 10.1016/j.tibtech.2006.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 04/18/2006] [Accepted: 06/02/2006] [Indexed: 11/30/2022]
Abstract
In Europe, in light of ethical, political and commercial pressure, every effort should be made to replace animals with alternatives (e.g. in vitro models), to reduce the number of animals used in experiments to a minimum and to refine current testing strategies in a way that ensures animals undergo minimum pain and distress. Methods currently used in toxicology for mandatory safety tests rely heavily on the dosing of animals, followed by the detection and pathological evaluation of manifested toxic lesions. Through the integration of so-called 'omics' technologies, a global analysis of treatment-related changes on the molecular level becomes feasible and therefore might provide a means for predicting toxicity before classical toxicological endpoints. This Opinion article summarizes the key features of pushing the '3R' principles in animal testing, discusses the possible impact on safety testing in toxicology and describes the potential of using omics technologies for improved toxicity prediction to meet ethical, political and commercial expectations.
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Affiliation(s)
- Michaela Kroeger
- Merck KGaA, Institute of Toxicology, Frankfurter Strasse 250, D-64293 Darmstadt, Germany.
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Yamamoto T, Kikkawa R, Yamada H, Horii I. Investigation of proteomic biomarkers in in vivo hepatotoxicity study of rat liver: toxicity differentiation in hepatotoxicants. J Toxicol Sci 2006; 31:49-60. [PMID: 16538043 DOI: 10.2131/jts.31.49] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We investigated the overall protein expression profiles in the in vivo hepatotoxicity of rats induced by four well-recognized hepatotoxicants. Acetaminophen (APAP), amiodarone (AMD), tetracycline (TC) and carbon tetrachloride (CTC) were administered to male rats by gavages and the liver at 24 hr post-dosing was applied to the proteomic experiment. Blood biochemistry and histopathology were examined to identify specific changes related to the compounds given. Protein expression in the liver was investigated by 2-dimensional gel electrophoresis (2DE), and spots showing a significantly different expression in treated versus control group were excised from gels and identified by Q-Tof mass spectrometer. They were well characterized based on their functions related to the mechanisms of toxicity of the compounds. Among them, we focused on the 8 proteins that were affected by all 4 compounds examined. Proteins related to oxidative stress response such as carbonic anhydrase III (CA3) and 60kDa heat shock protein (HSP60), and energy metabolism such as adenylate kinase 4 (AK4) were found. Moreover, hierarchical clustering analysis using 2D-gel spots information revealed the possibility to differentiate the groups based on their toxicity levels such as severity of liver damage. These results suggested that assessing the effects of hepatotoxicants on protein expression is worth trying to screen candidate compounds at the developmental stage of drugs.
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Affiliation(s)
- Toshinori Yamamoto
- Worldwide Safety Sciences, Pfizer Global Research & Development, Nagoya Laboratories, Pfizer Inc., 5-2 Taketoyo, Aichi 470-2393, Japan.
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Meistermann H, Norris JL, Aerni HR, Cornett DS, Friedlein A, Erskine AR, Augustin A, De Vera Mudry MC, Ruepp S, Suter L, Langen H, Caprioli RM, Ducret A. Biomarker discovery by imaging mass spectrometry: transthyretin is a biomarker for gentamicin-induced nephrotoxicity in rat. Mol Cell Proteomics 2006; 5:1876-86. [PMID: 16705188 DOI: 10.1074/mcp.m500399-mcp200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adverse drug effects are often associated with pathological changes in tissue. An accurate depiction of the undesired affected area, possibly supported by mechanistic data, is important to classify the effects with regard to relevance for human patients. MALDI imaging MS represents a new analytical tool to directly provide the spatial distribution and the relative abundance of proteins in tissue. Here we evaluate this technique to investigate potential toxicity biomarkers in kidneys of rats that were administered gentamicin, a well known nephrotoxicant. Differential analysis of the mass spectrum profiles revealed a spectral feature at 12,959 Da that strongly correlates with histopathology alterations of the kidney. We unambiguously identified this spectral feature as transthyretin (Ser(28)-Gln(146)) using an innovative combination of tissue microextraction and fractionation by reverse-phase liquid chromatography followed by a top-down tandem mass spectrometric approach. Our findings clearly demonstrate the emerging role of imaging MS in the discovery of toxicity biomarkers and in obtaining mechanistic insights concerning toxicity mechanisms.
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Affiliation(s)
- Hélène Meistermann
- Pharmaceuticals Division, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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Beyer S, Walter Y, Hellmann J, Kramer PJ, Kopp-Schneider A, Kroeger M, Ittrich C. Comparison of software tools to improve the detection of carcinogen induced changes in the rat liver proteome by analyzing SELDI-TOF-MS spectra. J Proteome Res 2006; 5:254-61. [PMID: 16457590 DOI: 10.1021/pr050279o] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A common animal model of chemical hepatocarcinogenesis was used to demonstrate the potential identification of carcinogenicity related protein signatures/biomarkers. Therefore, an animal study in which rats were treated with the known liver carcinogen N-nitrosomorpholine (NNM) or the corresponding vehicle was evaluated. Histopathological investigation as well as SELDI-TOF-MS analysis was performed. SELDI-TOF-MS is an affinity-based mass spectrometry method in which subsets of proteins from biological samples are selectively adsorbed to a chemically modified surface. The proteins are subsequently analyzed with respect to their mass-charge ratios (m/z) by a time of flight (TOF) mass spectrometry (MS) approach. As data preprocessing of SELDI-TOF-MS spectra is essential, baseline correction, normalization, peak detection, and alignment of raw spectra were performed using either the Ciphergen ProteinChip Software 3.1 or functions implemented in the library PROcess of the BioConductor Project. Baseline correction and normalization algorithms of both tools lead to comparable results, whereas results after peak detection and alignment steps differed. Variability between technical and biological replicates was investigated. A linear mixed model with factors experimental group and time point was applied for each protein peak, taking into account the different correlation structure of technical and biological replicates. Alternatively, only median intensity values of technical replicates were used. Results of both models were similar and correlated well with those of the histopathological evaluation of the study. In conclusion, statistical analyses lead to comparable results, whereas parameter settings for preprocessing proved to be crucial.
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Affiliation(s)
- Suse Beyer
- Institute of Toxicology, Merck KGaA, Darmstadt
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Abstract
We report on an observed regularity in the overall response of cell proteome under influence of different doses of a peroxisome proliferator. Our analysis for the first time demonstrates presence of hormesis at the cellular level. It is shown that despite the fact that the response of individual proteins remains unpredictable, the perturbation of proteome as a whole (measured as the average departure of protein abundances from the corresponding values of the control group) shows regularity: It initially decreases, reaches a minimum, and then increases as the concentration of the used proliferator continue to increase. The work is based on the available data of Anderson at al. on the effects of peroxisome proliferator LY171883 on protein abundances in mouse liver when administrated at different concentrations.
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Affiliation(s)
- Milan Randić
- Complex Systems Research Group, X-rays Unit, RIAIDT, Edificio CACTUS, University of Santiago de Compostela, Spain
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Kikkawa R, Fujikawa M, Yamamoto T, Hamada Y, Yamada H, Horii I. IN VIVO HEPATOTOXICITY STUDY OF RATS IN COMPARISON WITH IN VITRO HEPATOTOXICITY SCREENING SYSTEM. J Toxicol Sci 2006; 31:23-34. [PMID: 16538041 DOI: 10.2131/jts.31.23] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
For the establishment of a high throughput screening system using primary cell cultures, investigation of elucidated toxicities to assess the correlation between in vitro and in vivo hepatotoxicity is necessary in the safety evaluation of the compound. In the previous study, we reported the usability of rat primary cultured hepatocytes for establishment of high throughput screening system. To confirm the reliability of rat primary hepatocytes culture screening system, we conducted a single-dose in vivo study with relatively high dose of hepatotoxicant in rats using 4 reference compounds (acetaminophen, amiodarone, tetracycline, carbon tetrachloride), and investigated histopathological changes and expression of oxidative stress-related proteins by immunohistochemistry. We also carried out a proteomics analysis for estimating the reliable and sensitive biomarkers. Histopathologically, compound-specific hepatotoxicity was detected at 24 hr after administration in all compounds except amiodarone, which is known to induce phospholipidosis. Immunohistochemically, oxidative stress-related proteins were increased within 6 hr after administration in all treated groups. Proteomics analysis revealed several protein biomarkers related to oxidative stress and mitochondrial metabolism-regulation, which had been previously detected by proteomics analysis in in vitro screening system. Oxidative stress-related proteins were considered as useful biomarkers of hepatotoxicity; since they were detected by immunohistochemistry and proteomics analysis prior to appearance of compound-specific histopathological changes detected by light microscopy. Considering the relevance of in vitro system to in vivo system from the aspect of new biomarkers related to the toxicogenomics/toxicoproteomics, in vitro primary cell culture system would be sufficient to detect hepatotoxicity in the early stage of drug discovery.
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Affiliation(s)
- Rie Kikkawa
- Worldwide Safety Sciences, Pfizer Global Research and Development, Nagoya Laboratories, Pfizer Inc., 5-2 Taketoyo, Aichi 470-2393, Japan.
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Fella K, Glückmann M, Hellmann J, Karas M, Kramer PJ, Kröger M. Use of two-dimensional gel electrophoresis in predictive toxicology: identification of potential early protein biomarkers in chemically induced hepatocarcinogenesis. Proteomics 2005; 5:1914-27. [PMID: 15816005 DOI: 10.1002/pmic.200401067] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Our current approach focused on the identification of potential early protein biomarker signatures which are indicative of the carcinogenic processes in rats exposed to 20 mg/kg of the liver carcinogen N-nitrosomorpholine (NNM). Treated liver was investigated at different timepoints. Therefore, proteins were separated by two-dimensional gel electrophoresis as a first step prior to identification of differentially expressed proteins by mass spectrometry. Proteomic analysis of liver samples after one day of exposure revealed significant upregulation of proteins involved in response to cellular stress induced by NNM (superoxide dismutase, heat shock protein 60, peroxiredoxin). Eighteen weeks after withdrawal of NNM, we were able to identify cancer-related proteins in rat liver bearing malignant, transformed cells (caspase-8 precursor, vimentin, Rho GDP dissociation inhibitor). Some of these proteins were already deregulated after three weeks of exposure indicating their potential usefulness as early predictive biomarkers for liver carcinogenicity (annexin A5, fructose-1,6-bisphosphatase). As regulatory toxicology approaches usually include the investigation of carcinogenicity in two-years studies in rodents, especially the detection of early protein biomarker signatures which precede the appearance of neoplasia, demonstrates the high potential of proteomics approaches to substantially reduce the time and costs of carcinogenicity testing.
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Affiliation(s)
- Kerstin Fella
- Merck KGaA, Institute of Toxicology, Darmstadt, Germany
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Fu WY, Xu LH, Yu YN. Proteomic Analysis of Cellular Response to Microcystin in Human Amnion FL Cells. J Proteome Res 2005; 4:2207-15. [PMID: 16335968 DOI: 10.1021/pr050325k] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microcystins (MC), the potent inhibitor of protein phosphatase 1 and 2A, are hepatotoxins of increasing importance due to its high acute toxicity and potent tumor promoting activity. So far, the exact mechanisms of MC-induced hepatotoxicity and tumor promoting activity have not been fully elucidated. To better understand the mechanisms underlying microcystin-RR (MC-RR) induced toxicity as well as provide the possibility for the establishment of biomarkers for MC-RR exposure, differential proteome analysis on human amnion FL cells treated by MC-RR was carried out using two-dimensional gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Image analysis of silver-stained 2-dimensional gels revealed that 89 proteins showed significant differential expression in MC-RR treated cells compared with control, and 8 proteins were unique to MC-RR treated cells and 8 proteins were only detected in control cells. Sixty-six proteins were further identified with high confidence by peptide mass fingerprinting. Some of the identified differentially expressed proteins have clearly relationship with the process of apoptosis, signal transduction, and cytoskeleton alteration which are consistent with the literature. The functional implications of alterations in the levels of these proteins were discussed. However, most of which have not been reported previously to be involved in cellular processes responded to MC-RR. Therefore, this work will provide new insight into the mechanism of MC-RR toxicity.
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Affiliation(s)
- Wen-yu Fu
- Department of Biochemistry and Molecular Biology, Zhejiang University, School of Medicine, Hangzhou, China
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Gibbs A. Comparison of the specificity and sensitivity of traditional methods for assessment of nephrotoxicity in the rat with metabonomic and proteomic methodologies. J Appl Toxicol 2005; 25:277-95. [PMID: 16021680 DOI: 10.1002/jat.1064] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
There is currently a great deal of scientific interest and debate concerning the possible advantages that proteomic and metabonomic technologies might have over traditional biomarkers of toxicity (blood and urine chemistry, histopathology). Numerous papers have been published that make impressive claims concerning potential applications for these novel technologies, however there appears to be little hard evidence in the literature of their advantages over the traditional techniques for assessing toxicity. The aim of this review was to evaluate the relative sensitivity and specificity of proteomic and metabonomic techniques, compared with traditional techniques, for assessing xenobiotic-induced nephrotoxicity. A review of studies was performed where both one of the novel methods as well as traditional techniques were used for assessment of xenobiotic-induced nephrotoxicity. There was no consistent evidence from the literature that the novel methodologies were any more sensitive than the traditional methods for assessing nephrotoxicity. This could be due to the relatively small number of studies available for review (n = 13), the fact that generally these studies were not aimed at determining relative sensitivity or specificity and may not be the case with other target organs, such as the liver. However, it was clear that the novel methodologies were able to discriminate between the effects caused by different toxicants. There was evidence both that this discrimination was on the basis of different mechanisms of toxicity and on the basis of different locations of nephrotoxic lesion. A great deal of validation work is necessary before these techniques could gain full acceptance by regulatory authorities, and it is unclear whether their use in anything other than non-regulatory, mechanistic studies is likely to become widespread.
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Affiliation(s)
- Andy Gibbs
- Covance Laboratories Ltd, Otley Road, Harrogate, North Yorkshire HG3 1PY, UK.
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Witkamp RF. Genomics and systems biology - how relevant are the developments to veterinary pharmacology, toxicology and therapeutics? J Vet Pharmacol Ther 2005; 28:235-45. [PMID: 15953196 DOI: 10.1111/j.1365-2885.2005.00662.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This review discusses some of the recent developments in genomics and its current and future relevance for veterinary pharmacology and toxicology. With the rapid progress made in this field several new approaches in pharmacological and toxicological research have developed and drug discovery and drug development strategies have changed dramatically. In this review, the term genomics is used to encompass the three sub-disciplines transcriptomics, proteomics and metabolomics (or metabonomics) to describe the formation and fate of mRNA, proteins and metabolites, respectively. The current status and methods of the technology and some applications are briefly described. Although the DNA sequencing programmes are receiving considerable attention, the real value of genomics for pharmacology and toxicology is brought by the parallel developments in bio-informatics, bio-statistics and the integration of biology with mathematics and information technology. The ultimate level of integration is now mostly called systems biology, where mRNA, proteins and metabolites are being analysed in parallel, using a complete arsenal of analytical techniques (DNA-array, LC-MS/MS, GC-MS/MS, NMR, etc.). The information thus collected is analysed, integrated, linked to database information and translated to pathways and systems. This approach offers an enormous potential to study disease mechanisms and find new drug targets. Thus far, genomics and systems biology have not been introduced significantly in typical veterinary pharmacological and toxicological research programmes. The high costs and complexity connected to these large projects often form major obstacles for research groups with limited budgets. In other veterinary areas and disciplines, including infectious diseases, animal production and food-safety more examples of application are available. Genomics and bio-informatics provide outstanding opportunities to study pharmacology and toxicology in a more holistic way, taking into account the complexity of biological systems and based on the basic principles of physiology and the concept of homeostasis. Knowledge of biology, in vivo and in vitro models, and comparative pharmacology/toxicology is essential here, creating excellent opportunities for the veterinary trained scientist.
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