1
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Guillotin S, Delcourt N. Studying the Impact of Persistent Organic Pollutants Exposure on Human Health by Proteomic Analysis: A Systematic Review. Int J Mol Sci 2022; 23:ijms232214271. [PMID: 36430748 PMCID: PMC9692675 DOI: 10.3390/ijms232214271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Persistent organic pollutants (POPs) are organic chemical substances that are widely distributed in environments around the globe. POPs accumulate in living organisms and are found at high concentrations in the food chain. Humans are thus continuously exposed to these chemical substances, in which they exert hepatic, reproductive, developmental, behavioral, neurologic, endocrine, cardiovascular, and immunologic adverse health effects. However, considerable information is unknown regarding the mechanism by which POPs exert their adverse effects in humans, as well as the molecular and cellular responses involved. Data are notably lacking concerning the consequences of acute and chronic POP exposure on changes in gene expression, protein profile, and metabolic pathways. We conducted a systematic review to provide a synthesis of knowledge of POPs arising from proteomics-based research. The data source used for this review was PubMed. This study was carried out following the PRISMA guidelines. Of the 742 items originally identified, 89 were considered in the review. This review presents a comprehensive overview of the most recent research and available solutions to explore proteomics datasets to identify new features relevant to human health. Future perspectives in proteomics studies are discussed.
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Affiliation(s)
- Sophie Guillotin
- Poison Control Centre, Toulouse University Hospital, 31059 Toulouse, France
- INSERM UMR 1295, Centre d’Epidémiologie et de Recherche en Santé des Populations, 31000 Toulouse, France
| | - Nicolas Delcourt
- Poison Control Centre, Toulouse University Hospital, 31059 Toulouse, France
- INSERM UMR 1214, Toulouse NeuroImaging Center, 31024 Toulouse, France
- Correspondence: ; Tel.: +33-(0)-567691640
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2
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Andronis CE, Hane JK, Bringans S, Hardy GESJ, Jacques S, Lipscombe R, Tan KC. Gene Validation and Remodelling Using Proteogenomics of Phytophthora cinnamomi, the Causal Agent of Dieback. Front Microbiol 2021; 12:665396. [PMID: 34394023 PMCID: PMC8360494 DOI: 10.3389/fmicb.2021.665396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Phytophthora cinnamomi is a pathogenic oomycete that causes plant dieback disease across a range of natural ecosystems and in many agriculturally important crops on a global scale. An annotated draft genome sequence is publicly available (JGI Mycocosm) and suggests 26,131 gene models. In this study, soluble mycelial, extracellular (secretome), and zoospore proteins of P. cinnamomi were exploited to refine the genome by correcting gene annotations and discovering novel genes. By implementing the diverse set of sub-proteomes into a generated proteogenomics pipeline, we were able to improve the P. cinnamomi genome annotation. Liquid chromatography mass spectrometry was used to obtain high confidence peptides with spectral matching to both the annotated genome and a generated 6-frame translation. Two thousand seven hundred sixty-four annotations from the draft genome were confirmed by spectral matching. Using a proteogenomic pipeline, mass spectra were used to edit the P. cinnamomi genome and allowed identification of 23 new gene models and 60 edited gene features using high confidence peptides obtained by mass spectrometry, suggesting a rate of incorrect annotations of 3% of the detectable proteome. The novel features were further validated by total peptide support, alongside functional analysis including the use of Gene Ontology and functional domain identification. We demonstrated the use of spectral data in combination with our proteogenomics pipeline can be used to improve the genome annotation of important plant diseases and identify missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.
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Affiliation(s)
- Christina E Andronis
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia.,Proteomics International, Nedlands, WA, Australia
| | - James K Hane
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia.,Faculty of Science and Engineering, Curtin Institute for Computation, Curtin University, Perth, WA, Australia
| | | | - Giles E S J Hardy
- Centre for Phytophthora Science and Management, Murdoch University, Murdoch, WA, Australia
| | - Silke Jacques
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia
| | | | - Kar-Chun Tan
- Centre for Crop and Disease Management, Curtin University, Bentley, WA, Australia
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3
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Almeida MA, Almeida-Paes R, Guimarães AJ, Valente RH, Soares CMDA, Zancopé-Oliveira RM. Immunoproteomics Reveals Pathogen's Antigens Involved in Homo sapiens- Histoplasma capsulatum Interaction and Specific Linear B-Cell Epitopes in Histoplasmosis. Front Cell Infect Microbiol 2020; 10:591121. [PMID: 33251160 PMCID: PMC7673445 DOI: 10.3389/fcimb.2020.591121] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/07/2020] [Indexed: 12/15/2022] Open
Abstract
Histoplasmosis is one of the most frequent systemic mycosis in HIV patients. In these patients, histoplasmosis has high rates of morbidity/mortality if diagnosis and treatment are delayed. Despite its relevance, there is a paucity of information concerning the interaction between Histoplasma capsulatum and the human host, especially regarding the B-cell response, which has a direct impact on the diagnosis. Culture-based “gold-standard” methods have limitations, making immunodiagnostic tests an attractive option for clinical decisions. Despite the continuous development of those tests, improving serological parameters is necessary to make these methods efficient tools for definitive diagnosis of histoplasmosis. This includes the determination of more specific and immunogenic antigens to improve specificity and sensitivity of assays. In this study, we performed a co-immunoprecipitation assay between a protein extract from the yeast form of H. capsulatum and pooled sera from patients with proven histoplasmosis, followed by shotgun mass spectrometry identification of antigenic targets. Sera from patients with other pulmonary infections or from healthy individuals living in endemic areas of histoplasmosis were also assayed to determine potentially cross-reactive proteins. The primary structures of H. capsulatum immunoprecipitated proteins were evaluated using the DNAStar Protean 7.0 software. In parallel, the online epitope prediction server, BCPREDS, was used to complement the B-epitope prediction analysis. Our approach detected 132 reactive proteins to antibodies present in histoplasmosis patients’ sera. Among these antigens, 127 were recognized also by antibodies in heterologous patients’ and/or normal healthy donors’ sera. Therefore, the only three antigens specifically recognized by antibodies of histoplasmosis patients were mapped as potential antigenic targets: the M antigen, previously demonstrated in the diagnosis of histoplasmosis, and the catalase P and YPS-3 proteins, characterized as virulence factors of H. capsulatum, with antigenic properties still unclear. The other two proteins were fragments of the YPS-3 and M antigen. Overlapping results obtained from the two aforementioned bioinformatic tools, 16 regions from these three proteins are proposed as putative B-cell epitopes exclusive to H. capsulatum. These data reveal a new role for these proteins on H. capsulatum interactions with the immune system and indicate their possible use in new methods for the diagnosis of histoplasmosis.
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Affiliation(s)
- Marcos Abreu Almeida
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Rodrigo Almeida-Paes
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Allan Jefferson Guimarães
- Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense, Niterói, Brazil
| | - Richard Hemmi Valente
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Rosely Maria Zancopé-Oliveira
- Laboratório de Micologia, Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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4
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Prokopec SD, Viluksela M, Miettinen HM, Boutros PC, Pohjanvirta R. Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat. Arch Toxicol 2020; 94:1613-1624. [PMID: 32277265 DOI: 10.1007/s00204-020-02730-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
Abstract
In rats, direct exposure to TCDD causes myriad toxicities. Exposed rats experience hepatotoxicity, wasting syndrome and immune suppression, amongst others. "Inherited exposure", as occurs in the F3 generation of directly exposed F0 animals, has also been shown to cause toxicity: both male and female F3 rats demonstrate an increased incidence of adult onset disease, females also display reproductive abnormalities and increased incidence of ovarian diseases while males show increased incidence of kidney disease and an altered sperm epigenome. Here, we explore the hepatic transcriptomic profile of male and female F3 Sprague-Dawley rats bred through the paternal germ line from F0 dams exposed to a single dose of TCDD (0, 30, 100, 300 or 1000 ng/kg body weight) by oral gavage. We hypothesize that RNA transcripts with altered abundance in livers of unexposed F3 progeny of treated F0 Sprague-Dawley rats may result from epigenetic modifications to the genome. We further survey patterns of differential methylation within male F3 rat testis. Female F3 rats demonstrated more TCDD-mediated hepatic transcriptomic changes than males, with differences primarily in the lowest dose group. In testis from male F3 rats, multiple olfactory receptors displayed patterns of differential methylation. Hypermethylation of Egfr and Mc5r among testes from TCDD lineage rats was observed, but without corresponding changes in hepatic mRNA abundance. Further studies examining these differences in other tissue types are warranted.
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Affiliation(s)
| | - Matti Viluksela
- Department of Environmental and Biological Sciences, School of Pharmacy (Toxicology), University of Eastern Finland, Kuopio, Finland.,Environmental Health Unit, Finnish Institute for Health and Welfare (THL), Kuopio, Finland
| | - Hanna M Miettinen
- Environmental Health Unit, Finnish Institute for Health and Welfare (THL), Kuopio, Finland.,A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Canada. .,Department of Pharmacology and Toxicology, Universally of Toronto, Toronto, Canada. .,Department of Human Genetics, University of California, Los Angeles, 12-109 CHS, 10833 Le Conte Avenue, Los Angeles, CA, 90095, USA. .,Department of Urology, University of California, Los Angeles, Los Angeles, USA. .,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, USA. .,Institute for Precision Health, University of California, Los Angeles, Los Angeles, USA. .,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, USA.
| | - Raimo Pohjanvirta
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, P.O. Box 66, 00014, Helsinki, Finland.
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5
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Girolami F, Badino P, Spalenza V, Manzini L, Renzone G, Salzano AM, Dal Piaz F, Scaloni A, Rychen G, Nebbia C. Identification of candidate biomarkers of the exposure to PCBs in contaminated cattle: A gene expression- and proteomic-based approach. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 640-641:22-30. [PMID: 29852444 DOI: 10.1016/j.scitotenv.2018.05.284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
Dioxins and polychlorinated biphenyls (PCBs) are widespread and persistent contaminants. Through a combined gene expression/proteomic-based approach, candidate biomarkers of the exposure to such environmental pollutants in cattle subjected to a real eco-contamination event were identified. Animals were removed from the polluted area and fed a standard ration for 6 months. The decontamination was monitored by evaluating dioxin and PCB levels in pericaudal fat two weeks after the removal from the contaminated area (day 0) and then bimonthly for six months (days 59, 125 and 188). Gene expression measurements demonstrated that CYP1B1 expression was significantly higher in blood lymphocytes collected in contaminated animals (day 0), and decreased over time during decontamination. mRNA levels of interleukin 2 showed an opposite quantitative trend. MALDI-TOF-MS polypeptide profiling of serum samples ascertained a progressive decrease (from day 0 to 188) of serum levels of fibrinogen β-chain and serpin A3-7-like fragments, apolipoprotein (APO) C-II and serum amyloid A-4 protein, along with an augmented representation of transthyretin isoforms, as well as APOC-III and APOA-II proteins during decontamination. When differentially represented species were combined with serum antioxidant, acute phase and proinflammatory protein levels already ascertained in the same animals (Cigliano et al., 2016), bioinformatics unveiled an interaction network linking together almost all components. This suggests the occurrence of a complex PCB-responsive mechanism associated with animal contamination/decontamination, including a cohort of protein/polypeptide species involved in blood redox homeostasis, inflammation and lipid transport. All together, these results suggest the use in combination of such biomarkers for identifying PCB-contaminated animals, and for monitoring the restoring of their healthy condition following a decontamination process.
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Affiliation(s)
- F Girolami
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - P Badino
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - V Spalenza
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - L Manzini
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy
| | - G Renzone
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, Napoli, Italy
| | - A M Salzano
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, Napoli, Italy
| | - F Dal Piaz
- Department of Medicine and Surgery, University of Salerno, Via Giovanni Paolo II 132, Fisciano, Italy
| | - A Scaloni
- Proteomics and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, Napoli, Italy
| | - G Rychen
- Unité de Recherches Animal et Fonctionnalités des Produits Animaux, INRA-Université de Lorraine, 2 av de la forêt de Haye, Vandoeuvre-lès-Nancy Cedex, France
| | - C Nebbia
- Department of Veterinary Sciences, University of Torino, Largo P. Braccini 2, Grugliasco, Italy.
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6
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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7
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Crump D, Chiu S, Williams KL. Bis-(3-allyl-4-hydroxyphenyl) sulfone decreases embryonic viability and alters hepatic mRNA expression at two distinct developmental stages in chicken embryos exposed via egg injection. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2018; 37:530-537. [PMID: 28960418 DOI: 10.1002/etc.3990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/03/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Concerns surrounding the toxicological effects and environmental prevalence of bisphenol A (BPA) have increased efforts to identify suitable safer replacement alternatives. Bis-(3-allyl-4-hydroxyphenyl) sulfone (TGSH) represents a potential BPA alternative; however, exposure and ecotoxicological data are scarce. To determine effects on embryonic viability, development, and hepatic mRNA expression at 2 distinct developmental periods (midincubation [day 11] and pipping [days 20-21]), TGSH was injected into the air cell of unincubated, fertilized chicken embryos at 4 concentrations ranging from 0 to 180 μg/g egg. Concentrations of TGSH increased in a dose-dependent manner in whole-embryo homogenates, and the estimated median lethal dose (LD50) based on embryonic viability at midincubation was 66 µg/g (95% confidence interval = 31-142 µg/g), which is similar to the BPA LD50 (∼ 67 μg/g) reported in a previous study. Modulation of hepatic gene targets from a chicken ToxChip polymerase chain reaction (PCR) array was observed at both developmental stages. At midincubation, 21/43 genes on the PCR array were significantly altered (by >1.5-fold) in the 180 μg/g dose group, whereas 9 and 6/43 were altered at pipping in the 9.2 and 48 μg/g groups, respectively. Predominant toxicity pathways included xenobiotic metabolism, lipid homeostasis, bile acid synthesis, and cell cycle regulation. The estrogen-responsive gene apolipoprotein II was significantly up-regulated in liver tissue of midincubation embryos at 180 μg/g; however, neither apolipoprotein II nor vitellogenin II were altered at the other concentrations or developmental time points. Given the importance of identifying suitable BPA replacement alternatives, the present study provides novel, whole-animal toxicological data for a BPA replacement alternative that has an effect on embryonic viability similar to that of the compound it could replace. Environ Toxicol Chem 2018;37:530-537. © 2017 SETAC.
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Affiliation(s)
- Doug Crump
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Suzanne Chiu
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Kim L Williams
- National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
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8
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Nguyen HT, Tsuchiya MCL, Yoo J, Iida M, Agusa T, Hirano M, Kim EY, Miyazaki T, Nose M, Iwata H. Strain differences in the proteome of dioxin-sensitive and dioxin-resistant mice treated with 2,3,7,8-tetrabromodibenzo-p-dioxin. Arch Toxicol 2016; 91:1763-1782. [PMID: 27604104 DOI: 10.1007/s00204-016-1834-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/24/2016] [Indexed: 11/28/2022]
Abstract
Dioxins cause various toxic effects through the aryl hydrocarbon receptor (AHR) in vertebrates, with dramatic species and strain differences in susceptibility. Although inbred mouse strains C3H/HeJ-lpr/lpr (C3H/lpr) and MRL/MpJ-lpr/lpr (MRL/lpr) are known as dioxin-sensitive and dioxin-resistant mice, respectively, the molecular mechanism underlying this difference remains unclear. The difference in the hepatic proteome of the two mouse strains treated with vehicle or 2,3,7,8-tetrabromodibenzo-p-dioxin (TBDD) was investigated by a proteomic approach of two-dimensional electrophoresis (2-DE) coupled with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight tandem mass spectrometry (MALDI-TOF/TOF). To confirm the strain-difference in response to TBDD treatment, cytochrome P450 (CYP) 1A1 and 1A2 protein levels were measured in both strains. A dose of 10 µg/kg body weight of TBDD induced hepatic CYP1A1 and CYP1A2 expression in both strains, but the expression levels of both CYP1A proteins were higher in C3H/lpr mice than in MRL/lpr mice, supporting that C3H/lpr mice are more sensitive to dioxins than MRL/lpr mice. Proteins that were more induced or suppressed by TBDD treatment in C3H/lpr mice were successfully identified by 2-DE and MALDI-TOF/TOF, including proteins responsible for AHR activation through production of endogenous ligands such as aspartate aminotransferase, indolethylamine N-methyltransferase, and aldehyde dehydrogenases, as well as proteins reducing oxidative stress, such as superoxide dismutase and peroxiredoxins. Taken together, our results provide insights into the molecular mechanism underlying the high dioxin susceptibility of the C3H/lpr strain, in which AHR activation by TBDD is more prompted by the production of endogenous ligands, but the adaptation to oxidative stress is also acquired.
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Affiliation(s)
- Hoa Thanh Nguyen
- Laboratory of Environmental Toxicology, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan
| | - Maria Claret Lauan Tsuchiya
- Laboratory of Environmental Toxicology, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan.,Institute of Biological Sciences, University of the Philippines Los Baños, Laguna, Philippines
| | - Jean Yoo
- Laboratory of Environmental Toxicology, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan
| | - Midori Iida
- Graduate School of Computer Science and System Engineering, Kyushu Institute of Technology, Iizuka, 820-0067, Japan
| | - Tetsuro Agusa
- Laboratory of Environmental Toxicology, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan.,Graduate School of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto, 862-8502, Japan
| | - Masashi Hirano
- Laboratory of Environmental Toxicology, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan
| | - Eun-Young Kim
- Department of Life and Nanopharmaceutical Science and Department of Biology, Kyung Hee University, Seoul, 130-701, Korea
| | | | - Masato Nose
- Institute for Promotion of Advanced Science and Technology, Ehime University, Matsuyama, 790-8577, Japan
| | - Hisato Iwata
- Laboratory of Environmental Toxicology, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, 790-8577, Japan.
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9
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Evaluation of toxicological biomarkers in secreted proteins of HepG2 cells exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin and their expressions in the plasma of rats and incineration workers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:584-93. [DOI: 10.1016/j.bbapap.2016.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 02/16/2016] [Accepted: 02/22/2016] [Indexed: 11/21/2022]
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10
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Prokopec SD, Watson JD, Pohjanvirta R, Boutros PC. Identification of reference proteins for Western blot analyses in mouse model systems of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) toxicity. PLoS One 2014; 9:e110730. [PMID: 25329058 PMCID: PMC4201576 DOI: 10.1371/journal.pone.0110730] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 09/24/2014] [Indexed: 01/15/2023] Open
Abstract
Western blotting is a well-established, inexpensive and accurate way of measuring protein content. Because of technical variation between wells, normalization is required for valid interpretation of results across multiple samples. Typically this involves the use of one or more endogenous controls to adjust the measured levels of experimental molecules. Although some endogenous controls are widely used, validation is required for each experimental system. This is critical when studying transcriptional-modulators, such as toxicants like 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD).To address this issue, we examined hepatic tissue from 192 mice representing 47 unique combinations of strain, sex, Ahr-genotype, TCDD dose and treatment time. We examined 7 candidate reference proteins in each animal and assessed consistency of protein abundance through: 1) TCDD-induced fold-difference in protein content from basal levels, 2) inter- and intra- animal stability, and 3) the ability of each candidate to reduce instability of the other candidates. Univariate analyses identified HPRT as the most stable protein. Multivariate analysis indicated that stability generally increased with the number of proteins used, but gains from using >3 proteins were small. Lastly, by comparing these new data to our previous studies of mRNA controls on the same animals, we were able to show that the ideal mRNA and protein control-genes are distinct, and use of only 2–3 proteins provides strong stability, unlike in mRNA studies in the same cohort, where larger control-gene batteries were needed.
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Affiliation(s)
- Stephenie D. Prokopec
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John D. Watson
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Raimo Pohjanvirta
- Laboratory of Toxicology, National Institute for Health and Welfare, Kuopio, Finland
- Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland
| | - Paul C. Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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11
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Hu M, Liu Y, Yu K, Liu X. Decreasing the amount of trypsin in in-gel digestion leads to diminished chemical noise and improved protein identifications. J Proteomics 2014; 109:16-25. [DOI: 10.1016/j.jprot.2014.06.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/13/2014] [Accepted: 06/20/2014] [Indexed: 11/26/2022]
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12
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Miller I, Serchi T, Murk AJ, Gutleb AC. The added value of proteomics for toxicological studies. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2014; 17:225-246. [PMID: 24828453 DOI: 10.1080/10937404.2014.904730] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Proteomics has the potential to elucidate complex patterns of toxic action attributed to its unique holistic a posteriori approach. In the case of toxic compounds for which the mechanism of action is not completely understood, a proteomic approach may provide valuable mechanistic insight. This review provides an overview of currently available proteomic techniques, including examples of their application in toxicological in vivo and in vitro studies. Future perspectives for a wider application of state-of-the-art proteomic techniques in the field of toxicology are discussed. The examples concern experiments with dioxins, polychlorinated biphenyls, and polybrominated diphenyl ethers as model compounds, as they exhibit a plethora of sublethal effects, of which some mechanisms were revealed via successful proteomic studies. Generally, this review shows the added value of including proteomics in a modern tool box for toxicological studies.
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Affiliation(s)
- I Miller
- a Institute for Medical Biochemistry, Department for Biomedical Sciences , University of Veterinary Medicine Vienna , Vienna , Austria
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13
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O'Kane AA, Chevallier OP, Graham SF, Elliott CT, Mooney MH. Metabolomic profiling of in vivo plasma responses to dioxin-associated dietary contaminant exposure in rats: implications for identification of sources of animal and human exposure. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:5409-5418. [PMID: 23586690 DOI: 10.1021/es305345u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Dioxin contamination of the food chain typically occurs when cocktails of combustion residues or polychlorinated biphenyl (PCB) containing oils become incorporated into animal feed. These highly toxic compounds are bioaccumulative with small amounts posing a major health risk. The ability to identify animal exposure to these compounds prior to their entry into the food chain may be an invaluable tool to safeguard public health. Dioxin-like compounds act by a common mode of action and this suggests that markers or patterns of response may facilitate identification of exposed animals. However, secondary co-contaminating compounds present in typical dioxin sources may affect responses to compounds. This study has investigated for the first time the potential of a metabolomics platform to distinguish between animals exposed to different sources of dioxin contamination through their diet. Sprague-Dawley rats were given feed containing dioxin-like toxins from hospital incinerator soot, a common PCB oil standard and pure 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (normalized at 0.1 μg/kg TEQ) and acquired plasma was subsequently biochemically profiled using ultra high performance liquid chromatography (UPLC) quadropole time-of-flight-mass spectrometry (QTof-MS). An OPLS-DA model was generated from acquired metabolite fingerprints and validated which allowed classification of plasma from individual animals into the four dietary exposure study groups with a level of accuracy of 97-100%. A set of 24 ions of importance to the prediction model, and which had levels significantly altered between feeding groups, were positively identified as deriving from eight identifiable metabolites including lysophosphatidylcholine (16:0) and tyrosine. This study demonstrates the enormous potential of metabolomic-based profiling to provide a powerful and reliable tool for the detection of dioxin exposure in food-producing animals.
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Affiliation(s)
- Anthony A O'Kane
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast , David Keir Building, Stranmillis Road, Belfast, Northern Ireland, UK.
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14
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Mikkat S, Kischstein T, Kreutzer M, Glocker MO. Mass spectrometric peptide analysis of 2DE-separated mouse spinal cord and rat hippocampus proteins suggests an NGxG motif of importance for in vivo deamidation. Electrophoresis 2013; 34:1610-8. [DOI: 10.1002/elps.201200682] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 02/11/2013] [Accepted: 02/20/2013] [Indexed: 12/16/2022]
Affiliation(s)
| | - Timo Kischstein
- Oscar Langendorff Institute of Physiology; University Medicine Rostock; Rostock; Germany
| | - Michael Kreutzer
- Proteome Center Rostock; University Medicine Rostock; Rostock; Germany
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15
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Scornavacca G, Gesuete R, Orsini F, Pastorelli R, Fanelli R, de Simoni MG, Airoldi L. Proteomic analysis of mouse brain cortex identifies metabolic down-regulation as a general feature of ischemic pre-conditioning. J Neurochem 2012; 122:1219-29. [DOI: 10.1111/j.1471-4159.2012.07874.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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16
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Jubendradass R, D’Cruz SC, Judith Amala Rani S, Mathur P. Nonylphenol induces apoptosis via mitochondria- and Fas-l-mediated pathways in the liver of adult male rat. Regul Toxicol Pharmacol 2012; 62:405-11. [DOI: 10.1016/j.yrtph.2012.01.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Revised: 01/19/2012] [Accepted: 01/19/2012] [Indexed: 11/16/2022]
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17
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Brunelli L, Campagna R, Airoldi L, Cauli O, Llansola M, Boix J, Felipo V, Pastorelli R. Exploratory investigation on nitro- and phospho-proteome cerebellum changes in hyperammonemia and hepatic encephalopathy rat models. Metab Brain Dis 2012; 27:37-49. [PMID: 22083566 DOI: 10.1007/s11011-011-9268-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 10/25/2011] [Indexed: 01/15/2023]
Abstract
Hepatic encephalopathy (HE) is a neurological disease associated with hepatic dysfunction. Current knowledge suggests that hyperammonemia, related to liver failure, is a main factor contributing to the cerebral alterations in HE and that hyperammonemia might impair signal transduction associated with post-translational modification of proteins such as tyrosine-nitration and phosphorylation. However, the molecular bases of the HE remain unclear and very little is known about the occurrence of post-translational modification on in vivo proteins. In this exploratory study we look for evidence of post-translation modifications of proteins in the cerebellum of experimental HE rat models using a proteomic approach. For the first time we showed that hyperammonemia without liver failure (HA rats) and experimental HE with liver failure due to portacaval shunt (PCS rats) lead to a reduced protein nitration in rat cerebellum, where the undernitrated proteins were involved in energy metabolism and cytoskeleton remodelling. Moreover we showed that tyrosine nitration loss of these proteins was not necessarily associated to a change in their phosphorylation state as result of the disease. Interestingly the rat cerebellum phosphoproteome was mainly perturbed in PCS rats, whereas HA rats did not shown appreciable changes in their phosphoprotein profile. Since the protein nitration level decreased similarly in the cerebellum of both HA and PCS rats, this implies that the two disease models share common effects but also present some differential signalling effects in the cerebellum of the same animals. This study highlights the interest for studying the concerted action of multiple signalling pathways in HE development.
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Affiliation(s)
- Laura Brunelli
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy
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18
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Pan TL, Wang PW, Chen CC, Fang JY, Sintupisut N. Functional proteomics reveals hepatotoxicity and the molecular mechanisms of different forms of chromium delivered by skin administration. Proteomics 2012; 12:477-89. [DOI: 10.1002/pmic.201100055] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 11/09/2011] [Accepted: 11/17/2011] [Indexed: 12/11/2022]
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Li ZH, Li P, Sulc M, Hulak M, Randak T. Hepatic proteome sensitivity in rainbow trout after chronically exposed to a human pharmaceutical verapamil. Mol Cell Proteomics 2011; 11:M111.008409. [PMID: 21997734 DOI: 10.1074/mcp.m111.008409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Verapamil (VRP), a cardiovascular pharmaceutical widely distributed and persistent in the aquatic environment, has potential toxicity to fish and other aquatic organisms. However, the molecular mechanisms that lead to these toxic effects are not well known. In the present study, proteomic analysis has been performed to investigate the protein patterns that are differentially expressed in liver of rainbow trout exposed to sublethal concentrations of VRP (0.5, 27.0, and 270 μg/liter) for 42 days. Two-dimensional electrophoresis coupled with MALDI-TOF/TOF mass spectrometry was employed to detect and identify the protein profiles. The analysis revealed that the expression of six hepatic acidic proteins were markedly altered in the treatment groups compared with the control group; three proteins especially were significantly down-regulated in fish exposed to VRP at environmental related concentration (0.5 μg/liter). These results suggested that the VRP induce mechanisms against oxidative stress (glucose-regulated protein 78 and 94 and protein disulfide-isomerase A3) and adaptive changes in ion transference regulation (calreticulin, hyperosmotic glycine-rich protein). Furthermore, for the first time, protein Canopy-1 was found to be significantly down-regulated in fish by chronic exposure to VRP at environmental related levels. Overall, our work supports that fish hepatic proteomics analysis serves as an in vivo model for monitoring the residual pharmaceuticals in aquatic environment and can provide valuable insight into the molecular events in VRP-induced toxicity in fish and other organisms.
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Affiliation(s)
- Zhi-Hua Li
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jingzhou 434000, China.
| | - Ping Li
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Jingzhou 434000, China
| | - Miroslav Sulc
- Institute of Microbiology, AS CR, v.v.i., Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Martin Hulak
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
| | - Tomas Randak
- University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zatisi 728/II, 389 25 Vodnany, Czech Republic
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20
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Liu Y, Tam NFY, Guan Y, Yasojima M, Zhou J, Gao B. Acute toxicity of nonylphenols and bisphenol A to the embryonic development of the abalone Haliotis diversicolor supertexta. ECOTOXICOLOGY (LONDON, ENGLAND) 2011; 20:1233-1245. [PMID: 21479784 DOI: 10.1007/s10646-011-0672-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/29/2011] [Indexed: 05/30/2023]
Abstract
Acute toxic effects and mechanisms of two typical endocrine disrupting chemicals, nonylphenols (NPs) and bisphenol A (BPA), to the embryonic development of the abalone Haliotis diversicolor supertexta, were investigated by the two-stage embryo toxicity test. The 12-h median effective concentrations (EC(50)) of NPs and BPA to the trochophore development were 1016.22 and 30.72 μg L(-1), respectively, and the respective 96-h EC(50) values based on the completion of metamorphosis (another experimental endpoint) were reduced to 11.65 and 1.02 μg L(-1). Longer exposure time and magnified exposure concentrations in the benthic diatom, that serves as both food source and settlement substrate during the metamorphosis, via bioaccumulation, led to the higher sensitivity of metamorphosis to target EDCs compared with the trochophore development. The hazard concentrations for 5% of the species (HC(5)) could be employed as the safety thresholds for the embryonic development of the abalone. The 12-h HC(5) values of NPs and BPA were 318.68 and 13.93 μg L(-1), respectively, and the respective 96-h HC(5) values were 0.99 and 0.18 μg L(-1), which were at environmentally relevant levels. Results of proteomic responses revealed that NPs and BPA altered various functional proteins in the abalone larvae with slight differences between each chemical and affected various physiological functions, such as energy and substance metabolism, cell signalling, formation of cytoskeleton and cilium, immune and stress responses at the same time, leading to the failure of metamorphosis.
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Affiliation(s)
- Ying Liu
- Research Center of Environmental Engineering and Management, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, People's Republic of China
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21
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Mazzoletti M, Bortolin F, Brunelli L, Pastorelli R, Di Giandomenico S, Erba E, Ubezio P, Broggini M. Combination of PI3K/mTOR Inhibitors: Antitumor Activity and Molecular Correlates. Cancer Res 2011; 71:4573-84. [DOI: 10.1158/0008-5472.can-10-4322] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Li G, Chen J, Xie P, Jiang Y, Wu L, Zhang X. Protein expression profiling in the zebrafish (Danio rerio
) embryos exposed to the microcystin-LR. Proteomics 2011; 11:2003-18. [DOI: 10.1002/pmic.201000442] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 01/22/2011] [Accepted: 02/01/2011] [Indexed: 11/06/2022]
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23
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Schmitz-Spanke S, Rettenmeier AW. Protein expression profiling in chemical carcinogenesis: A proteomic-based approach. Proteomics 2011; 11:644-56. [DOI: 10.1002/pmic.201000403] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 10/12/2010] [Accepted: 10/15/2010] [Indexed: 11/11/2022]
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24
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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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25
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Iff J, Wang W, Sajic T, Oudry N, Gueneau E, Hopfgartner G, Varesio E, Szanto I. Differential proteomic analysis of STAT6 knockout mice reveals new regulatory function in liver lipid homeostasis. J Proteome Res 2010; 8:4511-24. [PMID: 19663508 DOI: 10.1021/pr9003272] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Increased inflammatory signaling is a key feature of metabolic disorders. In this context, the role of increased pro-inflammatory signals has been extensively studied. By contrast, no efforts have been dedicated to study the contrasting scenario: the attenuation of anti-inflammatory signals and their role in metabolic homeostasis. IL-4 and IL-13 are anti-inflammatory cytokines signaling through the Signal Transducer and Activator of Transcription 6 (STAT6). Our study was aimed at evaluating the lack of STAT6 signaling on liver homeostasis. To this end we analyzed the liver proteome of wild type and STAT6 knock-out mice using 2D nanoscale LC-MS/MS with iTRAQ labeling technique. The coordinated changes in proteins identified by this quantitative proteome analysis indicated disturbed lipid homeostasis and a state of hepatocellular stress. Most significantly, the expression of the liver fatty acid binding protein (FABP1) was increased in the knock-out mice. In line with the elevated FABP1 expression we found latent liver lipid accumulation in the STAT6-deficient mice which was further aggravated when mice were challenged by a high fat diet. In conclusion, our study revealed a so far uncharacterized role for STAT6 in regulating liver lipid homeostasis and demonstrates the importance of anti-inflammatory signaling in the defense against the development of liver steatosis.
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Affiliation(s)
- Joël Iff
- Department of Cellular Physiology and Metabolism, University of Geneva, Switzerland
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26
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Laloo B, Simon D, Veillat V, Lauzel D, Guyonnet-Duperat V, Moreau-Gaudry F, Sagliocco F, Grosset C. Analysis of post-transcriptional regulations by a functional, integrated, and quantitative method. Mol Cell Proteomics 2010; 8:1777-88. [PMID: 19411282 DOI: 10.1074/mcp.m800503-mcp200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the past 10 years, transcriptome and proteome analyses have provided valuable data on global gene expression and cell functional networks. However, when integrated,these analyses revealed partial correlations between mRNA expression levels and protein abundance thus suggesting that post-transcriptional regulations may be in part responsible for this discrepancy. In the present work, we report the development of a functional, integrated, and quantitative method to measure post-transcriptional regulations that we named FunREG. This method enables (i) quantitative measure of post-transcriptional regulations mediated by selected 3-untranslated regions and exogenous small interfering-RNA or micro-RNAs and (ii) comparison of these regulatory processes in physiologically relevant systems (e.g. cancer versus primary untransformed cells). We applied FunREG to the study of liver cancer, and we demonstrate for the first time the differential regulatory mechanisms controlling gene expression at a post-transcriptional level in normal and tumoral hepatic cells. As an example, translation efficiency mediated by heparin-binding epidermal growth factor 3-untranslated region was increased 3-fold in liver cancer cells compared with normal hepatocytes, whereas stability of an mRNA containing a portion of Cyclin D1 3-untranslated region was increased more than 2-fold in HepG2 cells compared with normal hepatocytes. Consequently we believe that the method presented herein may become an important tool in fundamental and medical research. This approach is convenient and easy to perform, accessible to any investigator, and should be adaptable to a large number of cell type, functional and chemical screens, as well as genome scale analyses. Finally FunREG may represent a helpful tool to reconcile transcriptome and proteome data.
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Affiliation(s)
- Benoît Laloo
- INSERM, U889, Groupe de Recherche pour l'Etude du Foie (GREF), Bordeaux, F-33076 France
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27
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Ji B, Zhang Z, Zhang M, Zhu H, Zhou K, Yang J, Li Y, Sun L, Feng G, Wang Y, He L, Wan C. Differential expression profiling of the synaptosome proteome in a rat model of antipsychotic resistance. Brain Res 2009; 1295:170-8. [DOI: 10.1016/j.brainres.2009.07.097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Revised: 06/30/2009] [Accepted: 07/24/2009] [Indexed: 11/17/2022]
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28
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Ji B, La Y, Gao L, Zhu H, Tian N, Zhang M, Yang Y, Zhao X, Tang R, Ma G, Zhou J, Meng J, Ma J, Zhang Z, Li H, Feng G, Wang Y, He L, Wan C. A comparative proteomics analysis of rat mitochondria from the cerebral cortex and hippocampus in response to antipsychotic medications. J Proteome Res 2009; 8:3633-41. [PMID: 19441803 DOI: 10.1021/pr800876z] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An increasing number of experiments have found anomalies in mitochondria in the brains of psychotics, which suggests that mitochondrial dysfunction or abnormal cerebral energy metabolism might play an important role in the pathophysiology of schizophrenia (SCZ). We adopted a proteomic approach to identify the differential effects on the cerebral cortex and hippocampus mitochondrial protein expression of Sprague-Dawley (SD) rats by comparing exposure to typical and atypical antipsychotic medications. Differential mitochondrial protein expressions were assessed using two-dimensional (2D) gel electrophoresis for three groups with Chlorpromazine (CPZ), Clozapine (CLZ), quetiapine (QTP) and a control group. A total of 14 proteins, of which 6 belong to the respiratory electron transport chain (ETC) of oxidative phosphorylation (OXPHOS), showed significant changes in quantity including NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 10 (Ndufa10), NADH dehydrogenase (ubiquinone) flavoprotein 2 (Ndufv2), NADH dehydrogenase (ubiquinone) Fe-S protein 3 (Ndufs3), F1-ATPase beta subunit (Atp5b), ATPase, H+ transporting, lysosomal, beta 56/58 kDa, isoform 2 (Atp6v1b2) and ATPase, H+ transporting, V1 subunit A, isoform 1 (Atp6v1a1). The differential proteins subjected to 2D were assessed for levels of mRNA using quantitative real time PCR (Q-RT-PCR), and we also made partial use of Western blotting for assessing differential expression. The results of our study may help to explain variations in SD rats as well as in human response to antipsychotic drugs. In addition, they should improve our understanding of both the curative effects and side effects of antipsychotics and encourage new directions in SCZ research.
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Affiliation(s)
- Baohu Ji
- Bio-X Center, Shanghai Jiao Tong University, Shanghai, China
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Tenorio-Laranga J, Männistö PT, Karayiorgou M, Gogos JA, García-Horsman JA. Sex-dependent compensated oxidative stress in the mouse liver upon deletion of catechol O-methyltransferase. Biochem Pharmacol 2009; 77:1541-52. [DOI: 10.1016/j.bcp.2009.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 02/09/2009] [Accepted: 02/11/2009] [Indexed: 11/30/2022]
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Kiyosawa N, Ando Y, Manabe S, Yamoto T. Toxicogenomic biomarkers for liver toxicity. J Toxicol Pathol 2009; 22:35-52. [PMID: 22271975 PMCID: PMC3246017 DOI: 10.1293/tox.22.35] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Accepted: 11/26/2008] [Indexed: 12/15/2022] Open
Abstract
Toxicogenomics (TGx) is a widely used technique in the preclinical stage of drug development to investigate the molecular mechanisms of toxicity. A number of candidate TGx biomarkers have now been identified and are utilized for both assessing and predicting toxicities. Further accumulation of novel TGx biomarkers will lead to more efficient, appropriate and cost effective drug risk assessment, reinforcing the paradigm of the conventional toxicology system with a more profound understanding of the molecular mechanisms of drug-induced toxicity. In this paper, we overview some practical strategies as well as obstacles for identifying and utilizing TGx biomarkers based on microarray analysis. Since clinical hepatotoxicity is one of the major causes of drug development attrition, the liver has been the best documented target organ for TGx studies to date, and we therefore focused on information from liver TGx studies. In this review, we summarize the current resources in the literature in regard to TGx studies of the liver, from which toxicologists could extract potential TGx biomarker gene sets for better hepatotoxicity risk assessment.
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Affiliation(s)
- Naoki Kiyosawa
- Medicinal Safety Research Labs., Daiichi Sankyo Co., Ltd., 717 Horikoshi, Fukuroi, Shizuoka 437-0065, Japan
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31
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Carpi D, Korkalainen M, Airoldi L, Fanelli R, Hakansson H, Muhonen V, Tuukkanen J, Viluksela M, Pastorelli R. Dioxin-Sensitive Proteins in Differentiating Osteoblasts: Effects on Bone Formation In Vitro. Toxicol Sci 2009; 108:330-43. [DOI: 10.1093/toxsci/kfp021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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32
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Scaloni A, Codarin E, Di Maso V, Arena S, Renzone G, Tiribelli C, Quadrifoglio F, Tell G. Modern strategies to identify new molecular targets for the treatment of liver diseases: The promising role of Proteomics and Redox Proteomics investigations. Proteomics Clin Appl 2009; 3:242-62. [DOI: 10.1002/prca.200800169] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Indexed: 12/16/2022]
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Gillardin V, Silvestre F, Dieu M, Delaive E, Raes M, Thomé JP, Kestemont P. Protein expression profiling in the African clawed frog Xenopus laevis tadpoles exposed to the polychlorinated biphenyl mixture aroclor 1254. Mol Cell Proteomics 2008; 8:596-611. [PMID: 19011258 DOI: 10.1074/mcp.m800323-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Exposure to environmental pollutants such as polychlorinated biphenyls (PCBs) is now taken into account to partly explain the worldwide decline of amphibians. PCBs induce deleterious effects on developing amphibians including deformities and delays in metamorphosis. However, the molecular mechanisms by which they express their toxicity during the development of tadpoles are still largely unknown. A proteomics analysis was performed on developing Xenopus laevis tadpoles exposed from 2 to 5 days postfertilization to either 0.1 or 1 ppm Aroclor 1254, a PCB mixture. Two-dimensional DIGE with a minimal labeling method coupled to nanoflow liquid chromatography-tandem mass spectrometry was used to detect and identify proteins differentially expressed under PCBs conditions. Results showed that 59 spots from the 0.1 ppm Aroclor 1254 condition and 57 spots from the 1 ppm Aroclor 1254 condition displayed a significant increase or decrease of abundance compared with the control. In total, 28 proteins were identified. The results suggest that PCBs induce mechanisms against oxidative stress (peroxiredoxins 1 and 2), adaptative changes in the energetic metabolism (enolase 1, glycerol-3-phosphate dehydrogenase, and creatine kinase muscle and brain types), and the implication of the unfolded protein response system (glucose-regulated protein, 58 kDa). They also affect, at least at the highest concentration tested, the synthesis of proteins involved in normal cytogenesis (alpha-tropomyosin, myosin heavy chain, and alpha-actin). For the first time, proteins such as aldehyde dehydrogenase 7A1, CArG binding factor-A, prolyl 4-hydroxylase beta, and nuclear matrix protein 200 were also shown to be up-regulated by PCBs in developing amphibians. These data argue that protein expression reorganization should be taken into account while estimating the toxicological hazard of wild amphibian populations exposed to PCBs.
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Affiliation(s)
- Virginie Gillardin
- Unité de Recherche en Biologie des Organismes, Facultés Universitaires Notre-Dame de la Paix, Rue de Bruxelles 61, B-5000 Namur, Belgium
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Malatesta M, Boraldi F, Annovi G, Baldelli B, Battistelli S, Biggiogera M, Quaglino D. A long-term study on female mice fed on a genetically modified soybean: effects on liver ageing. Histochem Cell Biol 2008; 130:967-77. [PMID: 18648843 DOI: 10.1007/s00418-008-0476-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2008] [Indexed: 12/12/2022]
Abstract
Liver represents a suitable model for monitoring the effects of a diet, due to its key role in controlling the whole metabolism. Although no direct evidence has been reported so far that genetically modified (GM) food may affect health, previous studies on hepatocytes from young female mice fed on GM soybean demonstrated nuclear modifications involving transcription and splicing pathways. In this study, the effects of this diet were studied on liver of old female mice in order to elucidate possible interference with ageing. The morpho-functional characteristics of the liver of 24-month-old mice, fed from weaning on control or GM soybean, were investigated by combining a proteomic approach with ultrastructural, morphometrical and immunoelectron microscopical analyses. Several proteins belonging to hepatocyte metabolism, stress response, calcium signalling and mitochondria were differentially expressed in GM-fed mice, indicating a more marked expression of senescence markers in comparison to controls. Moreover, hepatocytes of GM-fed mice showed mitochondrial and nuclear modifications indicative of reduced metabolic rate. This study demonstrates that GM soybean intake can influence some liver features during ageing and, although the mechanisms remain unknown, underlines the importance to investigate the long-term consequences of GM-diets and the potential synergistic effects with ageing, xenobiotics and/or stress conditions.
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Affiliation(s)
- Manuela Malatesta
- Dipartimento di Scienze Morfologico-Biomediche, Sezione di Anatomia e Istologia, University of Verona, strada Le Grazie 8, 37134, Verona, Italy.
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Wu YD, Jiang L, Zhou Z, Zheng MH, Zhang J, Liang Y. CYP1A/regucalcin gene expression and edema formation in zebrafish embryos exposed to 2,3,7,8-Tetrachlorodibenzo-p-dioxin. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2008; 80:482-486. [PMID: 18470470 DOI: 10.1007/s00128-008-9395-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Accepted: 03/11/2008] [Indexed: 05/26/2023]
Abstract
In this study, zebrafish eggs were exposed to a relatively low concentration (50 pg/mL) of 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) for 72 h and then transferred to vehicle/TCDD-free water for the remainder of the experiments. Mortality, heart rates, edema severity, CYP1A, and regucalcin gene expressions were investigated to study TCDD-induced toxicity in zebrafish during the early life stage. Results indicated that the 50 pg/mL TCDD caused severe and visible developmental toxicity. Further research of the long term and low concentration of TCDD exposure is required.
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Affiliation(s)
- Y D Wu
- Key Lab of Subtropical Agriculture and Environment, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, People's Republic of China.
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Poirrier JE, Guillonneau F, Renaut J, Sergeant K, Luxen A, Maquet P, Leprince P. Proteomic changes in rat hippocampus and adrenals following short-term sleep deprivation. Proteome Sci 2008; 6:14. [PMID: 18498662 PMCID: PMC2453108 DOI: 10.1186/1477-5956-6-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 05/22/2008] [Indexed: 11/10/2022] Open
Abstract
Background To identify the biochemical changes induced by sleep deprivation at a proteomic level, we compared the hippocampal proteome of rats either after 4 hours of sleep or sleep deprivation obtained by gentle handling. Because sleep deprivation might induce some stress, we also analyzed proteomic changes in rat adrenals in the same conditions. After sleep deprivation, proteins from both tissues were extracted and subjected to 2D-DIGE analysis followed by protein identification through mass spectrometry and database search. Results In the hippocampus, 87 spots showed significant variation between sleep and sleep deprivation, with more proteins showing higher abundance in the latter case. Of these, 16 proteins were present in sufficient amount for a sequencing attempt and among the 12 identified proteins, inferred affected cellular functions include cell metabolism, energy pathways, transport and vesicle trafficking, cytoskeleton and protein processing. Although we did not observe classical, macroscopic effect of stress in sleep-deprived rats, 47 protein spots showed significant variation in adrenal tissue between sleep and sleep deprivation, with more proteins showing higher abundance following sleep. Of these, 16 proteins were also present in sufficient amount for a sequencing attempt and among the 13 identified proteins, the most relevant cellular function that was affected was cell metabolism. Conclusion At a proteomic level, short term sleep deprivation is characterized by a higher expression of some proteins in the hippocampus and a lower abundance of other proteins in the adrenals (compared to normal sleep control). Altogether, this could indicate a general activation of a number of cellular mechanisms involved in the maintenance of wakefulness and in increased energy expenditure during sleep deprivation. These findings are relevant to suggested functions of sleep like energy repletion and the restoration of molecular stocks or a more global homeostasis of synaptic processes.
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Patterns of dioxin-altered mRNA expression in livers of dioxin-sensitive versus dioxin-resistant rats. Arch Toxicol 2008; 82:809-30. [PMID: 18465118 DOI: 10.1007/s00204-008-0303-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/02/2008] [Indexed: 12/11/2022]
Abstract
Dioxins exert their major toxicologic effects by binding to the aryl hydrocarbon receptor (AHR) and altering gene transcription. Numerous dioxin-responsive genes previously were identified both by conventional biochemical and molecular techniques and by recent mRNA expression microarray studies. However, of the large set of dioxin-responsive genes the specific genes whose dysregulation leads to death remain unknown. To identify specific genes that may be involved in dioxin lethality we compared changes in liver mRNA levels following exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in three strains/lines of dioxin-sensitive rats with changes in three dioxin-resistant rat strains/lines. The three dioxin-resistant strains/lines all harbor a large deletion in the transactivation domain of the aryl hydrocarbon receptor (AHR). Despite this deletion, many genes exhibited a "Type-I" response-that is, their responses were similar in dioxin-sensitive and dioxin-resistant rats. Several genes that previously were well established as being dioxin-responsive or under AHR regulation emerged as Type-I responses (e.g. CYP1A1, CYP1A2, CYP1B1 and Gsta3). In contrast, a relatively small number of genes exhibited a Type-II response-defined as a difference in responsiveness between dioxin-sensitive and dioxin-resistant rat strains. Type-II genes include: malic enzyme 1, ubiquitin C, cathepsin L, S-adenosylhomocysteine hydrolase and ferritin light chain 1. In silico searches revealed that AH response elements are conserved in the 5'-flanking regions of several genes that respond to TCDD in both the Type-I and Type-II categories. The vast majority of changes in mRNA levels in response to 100 microg/kg TCDD were strain-specific; over 75% of the dioxin-responsive clones were affected in only one of the six strains/lines. Selected genes were assessed by quantitative RT-PCR in dose-response and time-course experiments and responses of some genes were assessed in Ahr-null mice to determine if their response was AHR-dependent. Type-II genes may lie in pathways that are central to the difference in susceptibility to TCDD lethality in this animal model.
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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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Wei Y, Chan LL, Wang D, Zhang H, Wang J, Dai J. Proteomic Analysis of Hepatic Protein Profiles in Rare Minnow (Gobiocypris rarus) Exposed to Perfluorooctanoic Acid. J Proteome Res 2008; 7:1729-39. [DOI: 10.1021/pr7008059] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanhong Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Leo. L. Chan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Dazhi Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Hongxia Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Jianshe Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
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Applying gene expression, proteomics and single-nucleotide polymorphism analysis for complex trait gene identification. Genetics 2008; 178:1795-805. [PMID: 18245842 DOI: 10.1534/genetics.107.081216] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Previous quantitative trait locus (QTL) analysis of an intercross involving the inbred mouse strains NZB/BlNJ and SM/J revealed QTL for a variety of complex traits. Many QTL have large intervals containing hundreds of genes, and methods are needed to rapidly sort through these genes for probable candidates. We chose nine QTL: the three most significant for high-density lipoprotein (HDL) cholesterol, gallstone formation, and obesity. We searched for candidate genes using three different approaches: mRNA microarray gene expression technology to assess >45,000 transcripts, publicly available SNPs to locate genes that are not identical by descent and that contain nonsynonymous coding differences, and a mass-spectrometry-based proteomics technology to interrogate nearly 1000 proteins for differential expression in the liver of the two parental inbred strains. This systematic approach reduced the number of candidate genes within each QTL from hundreds to a manageable list. Each of the three approaches selected candidates that the other two approaches missed. For example, candidate genes such as Apoa2 and Acads had differential protein levels although the mRNA levels were similar. We conclude that all three approaches are important and that focusing on a single approach such as mRNA expression may fail to identify a QTL gene.
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Silkworth JB, Carlson EA, McCulloch C, Illouz K, Goodwin S, Sutter TR. Toxicogenomic Analysis of Gender, Chemical, and Dose Effects in Livers of TCDD- or Aroclor 1254–Exposed Rats Using a Multifactor Linear Model. Toxicol Sci 2008; 102:291-309. [DOI: 10.1093/toxsci/kfm313] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Oshima R, Nakano H, Katayama M, Sakurai J, Wu W, Koizumi S, Asano T, Watanabe T, Asakura T, Ohta T, Otsubo T. Modification of the hepatic mitochondrial proteome in response to ischemic preconditioning following ischemia-reperfusion injury of the rat liver. Eur Surg Res 2007; 40:247-55. [PMID: 18057903 DOI: 10.1159/000111982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2006] [Accepted: 09/03/2007] [Indexed: 01/02/2023]
Abstract
BACKGROUND/AIM Ischemic preconditioning (IPC) may reduce hepatic ischemia-reperfusion (IR) injury, but efficacy of IPC on mitochondrial proteome is not demonstrated. We investigated how IPC modifies the mitochondrial proteome after IR injury. METHODS Rats were subjected to 25 min of portal triad crossclamping (IR group, n = 8). In the IPC group (n = 8), 10 min of temporal portal triad clamping was performed before 25 min of portal clamping. Samples were obtained after 24 h. The mitochondrial inner-membrane potential was measured by the uptake of a lipophilic cationic carbocyanine probe and mitochondrial proteome was also investigated using 2-dimensional differential in-gel electrophoresis and liquid chromatography-tandem mass spectrometry. RESULTS Mitochondrial inner-membrane potential and glutathione were lower and serum transaminase was higher in the IPC group than in the IR group. The mitochondrial precursor of aldehyde dehydrogenase 2 and alpha-methylacyl-CoA-racemase were upregulated in the IPC group in comparison to the IR group. In contrast, protein disulfide-isomerase A3 precursor, 60S acid ribosomal protein P0, carbonic anhydrase 3 and superoxide dismutase were significantly more downregulated in the IPC group than in the IR group. CONCLUSIONS A hepatoprotective effect by IPC was not shown; however, IPC caused significant up- or downregulation of several mitochondrial proteins.
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Affiliation(s)
- R Oshima
- Division of Gastroenterological Surgery, St. Marianna University Hospital, Kawasaki, Japan
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Sarioglu H, Brandner S, Haberger M, Jacobsen C, Lichtmannegger J, Wormke M, Andrae U. Analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced proteome changes in 5L rat hepatoma cells reveals novel targets of dioxin action including the mitochondrial apoptosis regulator VDAC2. Mol Cell Proteomics 2007; 7:394-410. [PMID: 17998243 DOI: 10.1074/mcp.m700258-mcp200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
As part of a comprehensive survey of the impact of the environmental pollutant and hepatocarcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the proteome of hepatic cells, we have performed a high resolution two-dimensional gel electrophoresis study on the rat hepatoma cell line 5L. 78 protein species corresponding to 73 different proteins were identified as up- or down-regulated following exposure of the cells to 1 nm TCDD for 8 h. There was an overlap of only nine proteins with those detected as altered by TCDD in our recent study using the non-gel-based isotope-coded protein label method (Sarioglu, H., Brandner, S., Jacobsen, C., Meindl, T., Schmidt, A., Kellermann, J., Lottspeich, F., and Andrae, U. (2006) Quantitative analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels. Proteomics 6, 2407-2421) indicating a strong complementarity of the two approaches. For the majority of the altered proteins, an effect of TCDD on their abundance or posttranslational modifications had not been known before. Several observations suggest that a sizable fraction of the proteins with altered abundance was induced as an adaptive response to TCDD-induced oxidative stress that was demonstrated using the fluorescent probe dihydrorhodamine 123. A prominent group of these proteins comprised various enzymes for which there is evidence that their expression is regulated via the Keap1/Nrf2/antioxidant response element pathway. Other proteins included several involved in the maintenance of mitochondrial energy production and the regulation of the mitochondrial apoptotic pathway. A particularly intriguing finding was the up-regulation of the mitochondrial outer membrane pore protein, voltage-dependent anion channel-selective protein 2 (VDAC2), which was dependent on the presence of a functional aryl hydrocarbon receptor. The regulatability of VDAC2 protein abundance has not been described previously. In view of the recently discovered central role of VDAC2 as an inhibitor of the activation of the proapoptotic protein BAK and the mitochondrial apoptotic pathway, the present data point to a hitherto unrecognized mechanism by which TCDD may affect cellular homeostasis and survival.
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Affiliation(s)
- Hakan Sarioglu
- Institute of Toxicology, GSF-Research Center for Environment and Health, D-85764 Neuherberg, Germany
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Choi JS, Kim IW, Hwang SY, Shin BJ, Kim SK. Effect of 2,3,7,8-tetrachlorodibenzo-p-dioxin on testicular spermatogenesis-related panels and serum sex hormone levels in rats. BJU Int 2007; 101:250-5. [PMID: 17868417 DOI: 10.1111/j.1464-410x.2007.07202.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To determine the detrimental role of tetrachlorodibenzo-p-dioxin (TCDD) in testicular histology, spermatogenesis-related panels and proteome, and serum sex hormone levels. MATERIALS AND METHODS In all, 40 male rats were divided into equal groups: a normal control (NC) group that received vehicle and saline, and a TCDD-treated (TT) group injected intraperitoneally with TCDD (one dose, 50 microg/kg body weight). The rats were killed 4 weeks after TCDD exposure and testicular weight, histopathology, proteome and variables related to spermatogenesis, and serum sex hormone levels were investigated. RESULTS TCDD induced a significant decrease in testicular weight, Johnsen's score, seminiferous tubular size, percentage of tubules containing sperm, sperm counts, germ cell counts and Sertoli cell index. In addition, there was a significant decrease in serum testosterone level (P < 0.01) and a remarkable increase in oestradiol (P < 0.01), follicle-stimulating hormone (P < 0.05) and luteinizing hormone (P < 0.05) levels in the TT group. The expression of six testicular proteins including testis-specific heat shock protein (Hsp70), protein disulphide isomerase A3 precursor, 3-phosphoglycerate dehydrogenase, nonmuscle myosin heavy-chain type B-like protein, and superoxide dismutase 1 were significantly up-regulated (P < 0.05-0.01). Interestingly, fertility protein SP22 and phosphatidylethanolamine-binding protein were down-regulated but this was only significant for fertility protein SP22 (P < 0.05). CONCLUSION TCDD induces marked histological changes in the testis, impairs variables related to spermatogenesis, and increases serum oestradiol levels but decreases testosterone levels. In particular, TCDD disturbs testicular proteome profiles in rats.
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Affiliation(s)
- Jong-Soon Choi
- Proteomics Team, Korea Basic Science Institute, Taejeon, Korea
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Pastorelli R, Saletta F, Carpi D, Campagna R, dell'Osta C, Schiarea S, Vineis P, Airoldi L, Matullo G. Proteome characterization of a human urothelial cell line resistant to the bladder carcinogen 4-aminobiphenyl. Proteome Sci 2007; 5:6. [PMID: 17477866 PMCID: PMC1871571 DOI: 10.1186/1477-5956-5-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Accepted: 05/03/2007] [Indexed: 12/16/2022] Open
Abstract
Background The aromatic amine 4-aminobiphenyl (4-ABP) is an environmental and occupational contaminant known to be a major etiological agent of human bladder cancer. 4-ABP metabolites are able to form DNA adducts that may induce mutations and initiate bladder carcinogenesis. Cells exposed to 4-ABP may develop resistance to the carcinogen. The aim of the present study was to detect and identify proteins whose expression is altered in the bladder carcinoma RT112 sub-lines selected for acquired resistance to 4-ABP, in order to disentangle the mechanisms. Results Differential proteome analysis of cell lysates showed an overall perturbation in cell metabolism and energy pathways in the 4-ABP-resistant human urothelial clones, with over-expression of membrane trafficking proteins such as annexin 2. The resistant clones had altered expression of many proteins linked directly (i.e. lamin A/C, programmed cell death 6 interacting protein) or indirectly (i.e. 94 kDa glucose-regulated protein, fatty acid-binding protein) to decreased apoptosis, suggesting that resistance to 4-ABP might be associated with low apoptotic activity. Conclusion Our data provide evidence that deregulation of apoptosis and membrane trafficking proteins might be strongly implicated in the selection of carcinogen resistant cells. Some of these proteins might have potential as biomarkers of resistance and cancer risk.
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Affiliation(s)
- Roberta Pastorelli
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Federica Saletta
- Section of Life Sciences, Institute for Scientific Interchange Foundation, Torino, Italy
| | - Donatella Carpi
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Roberta Campagna
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Carlo dell'Osta
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Silvia Schiarea
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Paolo Vineis
- Department of Epidemiology and Public Health, Imperial College London, London, UK
- Department of Biomedical Sciences and Human Oncology, University of Torino, Torino, Italy
| | - Luisa Airoldi
- Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Giuseppe Matullo
- Section of Life Sciences, Institute for Scientific Interchange Foundation, Torino, Italy
- Department of Genetics, University of Torino, Torino, Italy
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Boverhof DR, Burgoon LD, Tashiro C, Sharratt B, Chittim B, Harkema JR, Mendrick DL, Zacharewski TR. Comparative toxicogenomic analysis of the hepatotoxic effects of TCDD in Sprague Dawley rats and C57BL/6 mice. Toxicol Sci 2006; 94:398-416. [PMID: 16960034 DOI: 10.1093/toxsci/kfl100] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In an effort to further characterize conserved and species-specific mechanisms of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)-mediated toxicity, comparative temporal and dose-response microarray analyses were performed on hepatic tissue from immature, ovariectomized Sprague Dawley rats and C57BL/6 mice. For temporal studies, rats and mice were gavaged with 10 or 30 microg/kg of TCDD, respectively, and sacrificed after 2, 4, 8, 12, 18, 24, 72, or 168 h while dose-response studies were performed at 24 h. Hepatic gene expression profiles were monitored using custom cDNA microarrays containing 8567 (rat) or 13,361 (mouse) cDNA clones. Affymetrix data from male rats treated with 40 microg/kg TCDD were also included to expand the species comparison. In total, 3087 orthologous genes were represented in the cross-species comparison. Comparative analysis identified 33 orthologous genes that were commonly regulated by TCDD as well as 185 rat-specific and 225 mouse-specific responses. Functional annotation using Gene Ontology identified conserved gene responses associated with xenobiotic/chemical stress and amino acid and lipid metabolism. Rat-specific gene expression responses were associated with cellular growth and lipid metabolism while mouse-specific responses were associated with lipid uptake/metabolism and immune responses. The common and species-specific gene expression responses were also consistent with complementary histopathology, clinical chemistry, hepatic lipid analyses, and reports in the literature. These data expand our understanding of TCDD-mediated gene expression responses and indicate that species-specific toxicity may be mediated by differences in gene expression which may help explain the wide range of species sensitivities and will have important implications in risk assessment strategies.
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Affiliation(s)
- Darrell R Boverhof
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Basso M, Massignan T, Samengo G, Cheroni C, De Biasi S, Salmona M, Bendotti C, Bonetto V. Insoluble mutant SOD1 is partly oligoubiquitinated in amyotrophic lateral sclerosis mice. J Biol Chem 2006; 281:33325-35. [PMID: 16943203 DOI: 10.1074/jbc.m603489200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mutations in the Cu,Zn-superoxide dismutase (SOD1) gene cause a familial form of amyotrophic lateral sclerosis (ALS) through an unknown gain-of-function mechanism. Mutant SOD1 aggregation may be the toxic property. In fact, proteinaceous inclusions rich in mutant SOD1 have been found in tissues from the familial form of ALS patients and in mutant SOD1 animals, before disease onset. However, very little is known of the constituents and mechanism of formation of aggregates in ALS. We and others have shown that there is a progressive accumulation of detergent-insoluble mutant SOD1 in the spinal cord of G93A SOD1 mice. To investigate the mechanism of SOD1 aggregation, we characterized by proteome technologies SOD1 isoforms in a Triton X-100-insoluble fraction of spinal cord from G93A SOD1 mice at different stages of the disease. This showed that at symptomatic stages of the disease, part of the insoluble SOD1 is unambiguously mono- and oligoubiquitinated, in spinal cord and not in hippocampus, and that ubiquitin branches at Lys(48), the major signal for proteasome degradation. At presymptomatic stages of the disease, only insoluble unmodified SOD1 is recovered. Partial ubiquitination of SOD1-rich inclusions was also confirmed by immunohistochemical and electron microscopy analysis of lumbar spinal cord sections from symptomatic G93A SOD1 mice. On the basis of these results, we propose that ubiquitination occurs only after SOD1 aggregation and that oligoubiquitination may underline alternative mechanisms in disease pathogenesis.
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