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Gianazza E, Miller I, Guerrini U, Palazzolo L, Parravicini C, Eberini I. Gender proteomics I. Which proteins in non-sexual organs. J Proteomics 2017; 178:7-17. [PMID: 28988882 DOI: 10.1016/j.jprot.2017.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Differences related to gender have long been neglected but recent investigations show that they are widespread and may be recognized with all types of omics approaches, both in tissues and in biological fluids. Our review compiles evidence collected with proteomics techniques in our species, mainly focusing on baseline parameters in non-sexual organs in healthy men and women. Data from human specimens had to be replaced with information from other mammals every time invasive procedures of sample procurement were involved. SIGNIFICANCE As our knowledge, and the methods to build it, get refined, gender differences need to receive more and more attention, as they influence the outcome of all aspects in lifestyle, including diet, exercise and environmental factors. In turn this background modulates a differential susceptibility to some disease, or a different pathogenetic mechanism, depending on gender, and a different response to pharmacological therapy. Preparing this review we meant to raise awareness about the gender issue. We anticipate that more and more often, in the future, separate evaluations will be carried out on male and female subjects as an alternative - and an upgrade - to the current approach of reference and test groups being 'matched for age and sex'.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy.
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
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2
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Miller I, Diepenbroek C, Rijntjes E, Renaut J, Teerds KJ, Kwadijk C, Cambier S, Murk AJ, Gutleb AC, Serchi T. Gender specific differences in the liver proteome of rats exposed to short term and low-concentration hexabromocyclododecane (HBCD). Toxicol Res (Camb) 2016; 5:1273-1283. [PMID: 30090431 PMCID: PMC6062380 DOI: 10.1039/c6tx00166a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/23/2016] [Indexed: 01/17/2023] Open
Abstract
The influence of short term (7-day) exposure of male rats to the brominated flame retardant hexabromocyclododecane (HBCD) was studied by investigation of the liver proteome, both in euthyroid and hypothyroid rats and by comparing results with general data on animal physiology and thyroid hormone, leptin, insulin and gonadotropin concentrations determined in parallel. Proteome analysis of liver tissue by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE) revealed that only small protein pattern changes were induced by exposure in males, on just a few proteins with different functions and not involved in pathways in common. This is in contrast to previous findings in similarly exposed eu- and hypothyroid female rats, where general metabolic pathways had been shown to be affected. The largest gender-dependent effects concerned basal concentrations of liver proteins already in control and hypothyroid animals, involving mainly the pathways which were also differently affected by HBCD exposure. Among them were differences in lipid metabolism, which - upon exposure to HBCD - may also be the reason for the considerably higher ratio of γ-HBCD accumulated in white adipose tissue of exposed female rats compared to males. The results further elucidate the already suggested different sensitivity of genders towards HBCD exposure on the protein level, and confirm the need for undertaking toxicological animal experiments in both genders.
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Affiliation(s)
- I Miller
- Institute for Medical Biochemistry , Department for Biomedical Sciences , University of Veterinary Medicine Vienna , Veterinaerplatz 1 , A-1210 Vienna , Austria .
| | - C Diepenbroek
- Wageningen University , Human and Animal Physiology , P.O. Box 338 , 6700 AH Wageningen , The Netherlands
| | - E Rijntjes
- Wageningen University , Human and Animal Physiology , P.O. Box 338 , 6700 AH Wageningen , The Netherlands
- Charité-Universitätsmedizin Berlin , Institute of Experimental Endocrinology , Augustenburger Platz 1 , 13353, Berlin , Germany
| | - J Renaut
- Environmental Research and Innovation (ERIN) Department , Luxembourg Institute of Science and Technology (LIST) , 5 , avenue des Hauts-Fourneaux , L-4362 Esch-sur-Alzette , Grand-duchy of Luxembourg . ; Tel: +352-470 261
| | - K J Teerds
- Wageningen University , Human and Animal Physiology , P.O. Box 338 , 6700 AH Wageningen , The Netherlands
| | - C Kwadijk
- Wageningen Institute for Marine Resources & Ecosystem Studies , IMARES , IJmuiden , The Netherlands
| | - S Cambier
- Environmental Research and Innovation (ERIN) Department , Luxembourg Institute of Science and Technology (LIST) , 5 , avenue des Hauts-Fourneaux , L-4362 Esch-sur-Alzette , Grand-duchy of Luxembourg . ; Tel: +352-470 261
| | - A J Murk
- Wageningen University , Marine Animal Ecology Group , De Elst 1 , 6708 WD Wageningen , The Netherlands
| | - A C Gutleb
- Environmental Research and Innovation (ERIN) Department , Luxembourg Institute of Science and Technology (LIST) , 5 , avenue des Hauts-Fourneaux , L-4362 Esch-sur-Alzette , Grand-duchy of Luxembourg . ; Tel: +352-470 261
| | - T Serchi
- Environmental Research and Innovation (ERIN) Department , Luxembourg Institute of Science and Technology (LIST) , 5 , avenue des Hauts-Fourneaux , L-4362 Esch-sur-Alzette , Grand-duchy of Luxembourg . ; Tel: +352-470 261
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3
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Optimized proteomic analysis of rat liver microsomes using dual enzyme digestion with 2D-LC–MS/MS. J Proteomics 2013; 82:166-78. [DOI: 10.1016/j.jprot.2013.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/24/2013] [Accepted: 02/08/2013] [Indexed: 12/23/2022]
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4
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Sun L, Zhang Y, Tao D, Zhu G, Zhao Q, Wu Q, Liang Z, Yang L, Zhang L, Zhang Y. SDS-PAGE-free protocol for comprehensive identification of cytochrome P450 enzymes and uridine diphosphoglucuronosyl transferases in human liver microsomes. Proteomics 2012; 12:3464-9. [DOI: 10.1002/pmic.201200260] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/04/2012] [Accepted: 09/20/2012] [Indexed: 12/11/2022]
Affiliation(s)
- Liangliang Sun
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Yanyan Zhang
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Dingyin Tao
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Guijie Zhu
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Qun Zhao
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
- Graduate School of Chinese Academy of Sciences; Beijing China
| | - Qi Wu
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
- Graduate School of Chinese Academy of Sciences; Beijing China
| | - Zhen Liang
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Lihua Zhang
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
| | - Yukui Zhang
- Laboratory of High Efficient Separation and High Sensitive Characterization of Biomolecules, Dalian Institute of Chemical Physics; Chinese Academy of Science; Dalian China
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5
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Moskaleva NE, Zgoda VG. [Current methods of cytochrome p450 analysis]. BIOMEDITSINSKAIA KHIMIIA 2012; 58:617-634. [PMID: 23350195 DOI: 10.18097/pbmc20125806617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Current review describes recent approaches of cytochrome P450 concentration and activity evaluation. Special attention paid to modem methods of proteomic analysis such as electrophoresis and chromato-mass-spectrometry. Methods of targeted proteomic applicable for quantitative and qualitative study of P450s in biological samples as well as methods for the enzyme activity measurements are reviewed. Finally, data on correlation between certain P450 isoform content and its specific enzymatic activities were described and discussed in the review.
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6
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Van Summeren A, Renes J, van Delft JH, Kleinjans JC, Mariman EC. Proteomics in the search for mechanisms and biomarkers of drug-induced hepatotoxicity. Toxicol In Vitro 2012; 26:373-85. [DOI: 10.1016/j.tiv.2012.01.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 12/22/2011] [Accepted: 01/09/2012] [Indexed: 10/14/2022]
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7
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Petushkova NA, Lisitsa AV. Producing a one-dimensional proteomic map for human liver cytochromes p450. Methods Mol Biol 2012; 909:63-82. [PMID: 22903709 DOI: 10.1007/978-1-61779-959-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this chapter we explore the inducible cytochrome P450 (CYP) forms as an example of membrane proteins analysis that relies on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) fractionation with subsequent mass spectrometric (MS) identification. The approach involves cutting an SDS-PAGE gel lane into thin slices and identifying proteins in each slice by MS with the aim of obtaining detailed information on proteins of interest. A one-dimensional proteomic map showing the distribution of selected CYP isoforms across 40 slices was constructed using mass spectra obtained from each slice. Our protocol proved to be efficient enough to obtain a comprehensive profile of drug-metabolizing enzymes in the human liver. In addition to human tissues, the approach described should be applicable to the characterization of membrane proteins in other eukaryotic species.
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Affiliation(s)
- Natalia A Petushkova
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Moscow, Russia.
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8
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Fu S, Rowe A, Ramzan I. Kavalactone Metabolism in Rat Liver Microsomes. Phytother Res 2011; 26:1057-61. [DOI: 10.1002/ptr.3695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/01/2011] [Accepted: 09/29/2011] [Indexed: 01/04/2023]
Affiliation(s)
- Shuang Fu
- Faculty of Pharmacy; University of Sydney; NSW; 2006; Australia
| | - Anthony Rowe
- Faculty of Pharmacy; University of Sydney; NSW; 2006; Australia
| | - Iqbal Ramzan
- Faculty of Pharmacy; University of Sydney; NSW; 2006; Australia
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9
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Huang HJ, Tsai ML, Chen YW, Chen SH. Quantitative shot-gun proteomics and MS-based activity assay for revealing gender differences in enzyme contents for rat liver microsome. J Proteomics 2011; 74:2734-44. [PMID: 21300189 DOI: 10.1016/j.jprot.2011.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/17/2011] [Accepted: 01/27/2011] [Indexed: 12/16/2022]
Abstract
Liver microsomes are subcellular fractions that contain many metabolizing enzymes for drugs and endogeneous compounds. Some of these enzymes are regulated by sex hormonal control and exhibit sex-dependent expression pattern and metabolizing speed. Studying these enzymes, however, are complicated by the presence of isoforms such as cytochrome P450 (CYP450), which families share more than 50% amino acid identities. In this study, we applied quantitative shot-gun proteomics approach coupled with stable-isotope dimethyl labeling, two-dimensional reversed-phase peptide separation and tandem mass spectrometry (MS) to explore the gender-dependent expression of rat liver microsomal proteins. A total of 391 proteins were identified and quantified by this approach, and 56% of quantified proteins were enzymes. Although shot-gun approach is rarely used for identifying protein isoforms, we identified 53 isoforms by at least one unique peptide including 21 isoforms of CYP450s. Moreover, by quantitative and statistics assessment, we were able to classify them into 28 male dominant enzymes including CYP2C12 CYP2C11, CYP2C13, CYP2B3, CYP2C11, CYP2C70 and CYP3A2 which are known to be male specific, 21 female dominant enzymes including CYP2A1, CYP2C7, CYP2C12, CYP2D26, alcohol dehydrogenase 1, carboxylesterase 3, glutathione S-transferase, liver carboxylesterase 4, UDP-glucuronosyltransferase 2B1, and glyceraldehyde-3-phosphate dehydrogenase which are known to be female specific; and 125 sex-independent enzymes. However, most of the sex specificities revealed from this study, such as the male specificity of CYP2D1, were novel and not yet reported. We then conducted a mass spectrometry-multiple reaction mode (MS-MRM) based enzyme activity method to determine the catalyzing rate of CYP2D1 in male and female liver microsomes using carteolol as its specific substrate. The reaction rate catalyzed by CYP2D1 in female rats was determined to differ significantly with the rate in male rats. Moreover, the ratio (female/male) of reaction rate (0.68) was found to correlate with their relative protein abundance (0.72). This study revealed novel sex dependences of many rat liver enzymes and also demonstrated a unique MS-based analytical platform that could identify novel iso-enzymes and further quantify their abundance and enzyme activity.
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Affiliation(s)
- Hung-Jen Huang
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
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10
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Yang F, Yin Y, Wang F, Zhang L, Wang Y, Sun S. An altered pattern of liver apolipoprotein A-I isoforms is implicated in male chronic hepatitis B progression. J Proteome Res 2010; 9:134-43. [PMID: 19788185 DOI: 10.1021/pr900593r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chronic hepatitis B (CHB) appears to progress more rapidly in males than in females, and CHB-related hepatic cirrhosis and hepatocellular carcinoma are predominately diseases that tend to occur in men and postmenopausal women. To obtain more insight into the underlying mechanisms of gender disparity of CHB progress, two-dimensional difference gel electrophoresis was employed to compare liver proteome of C57BL/6 and HBV transgenic (HBV-Tg) mice both in male and female groups. We identified 8 differently expressed proteins in male HBV-Tg mice and 12 in female HBV-Tg mice. Apolipoprotein A-I (Apo A-I) was found to be down-regulated in male and female HBV-Tg mouse liver. It is more interesting that the pattern of liver Apo A-I isoforms was altered in male HBV-Tg mice but not in female HBV-Tg mice. Our further results indicated that the basic Apo A-I isoform, based on pI positions from serum 2-dimensional Western blotting, increased in male CHB patient sera but not in female CHB patient sera. Finally, we identified that the oxidative modification Apo A-I mainly reside in basic isoform. This pattern of selectively modified Apo A-I isoforms may be considered as a pathological hallmark that may extend our knowledge of the molecular pathogenesis of CHB progression.
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Affiliation(s)
- Fu Yang
- Department of Medical Genetics, Second Military Medical University, Shanghai, China
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11
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Sutton CW, Sutherland M, Shnyder S, Patterson LH. Improved preparation and detection of cytochrome P450 isoforms using MS methods. Proteomics 2010; 10:327-31. [PMID: 19902426 DOI: 10.1002/pmic.200900489] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Cytochromes P450 (CYPs) are a superfamily of mixed function oxidases, which in the liver have great significance to the pharmaceutical industry because their expression will determine the fate of most clinical agents. CYPs are also targets for inhibitors of hormone-dependent diseases and conversion of prodrugs to active agents in normal and cancer tissues. We have applied simple modifications to established methods of isolating CYPs, using 8 M urea to solubilise microsomal proteins and specific molecular weight gel bands for in-gel digestion in combination with nanoHPLC MALDI MS to acquire peptide MS/MS spectra for database searching. As a consequence of the changes we significantly improved the yield of proteomic data, identifying 26 mouse CYPs (CYP1a2, 2a4, 2a5, 2a12, 2b9, 2c29, 2c37, 2c39, 2c40, 2c50, 2c54, 2c70, 2d9, 2d10, 2d26, 2e1, 2f2, 2j5, 3a11, 3a13, 3a25, 3a41, 4a14, 4f14, 8b1 and 27a1) with an average sequence coverage of 30.1%, including some previously undetected highly homologous isoforms. In addition, other important enzymes in drug metabolism are also identified. There is a divergence of opinion over the expression of CYP1a1 in liver and we could not detect the presence of this isoform. In order to provide definitive evidence of the ability to detect CYP1a1, we analysed CHO cells transfected with human CYP1A1 and identified unique peptides that differentiated this isoform from human CYP1A2.
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Affiliation(s)
- Chris W Sutton
- Institute of Cancer Therapeutics, University of Bradford, Bradford, West Yorkshire, BD7 1DP,UK.
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12
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Seibert C, Davidson BR, Fuller BJ, Patterson LH, Griffiths WJ, Wang Y. Multiple-approaches to the identification and quantification of cytochromes P450 in human liver tissue by mass spectrometry. J Proteome Res 2009; 8:1672-81. [PMID: 19714871 DOI: 10.1021/pr800795r] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Here we report the identification and approximate quantification of cytochrome P450 (CYP) proteins in human liver microsomes as determined by nano-LC-MS/MS with application of the exponentially modified protein abundance index (emPAI) algorithm during database searching. Protocols based on 1D-gel protein separation and 2D-LC peptide separation gave comparable results. In total, 18 CYP isoforms were unambiguously identified based on unique peptide matches. Further, we have determined the absolute quantity of two CYP enzymes (2E1 and 1A2) in human liver microsomes using stable-isotope dilution mass spectrometry, where microsomal proteins were separated by 1D-gel electrophoresis, digested with trypsin in the presence of either a CYP2E1- or 1A2-specific stable-isotope labeled tryptic peptide and analyzed by LC-MS/MS. Using multiple reaction monitoring (MRM) for the isotope-labeled tryptic peptides and their natural unlabeled analogues quantification could be performed over the range of 0.1-1.5 pmol on column. Liver microsomes from four individuals were analyzed for CYP2E1 giving values of 88-200 pmol/mg microsomal protein. The CYP1A2 content of microsomes from a further three individuals ranged from 165 to 263 pmol/mg microsomal protein. Although, in this proof-of-concept study for CYP quantification, the two CYP isoforms were quantified from different samples, there are no practical reasons to prevent multiplexing the method to allow the quantification of multiple CYP isoforms in a single sample.
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Affiliation(s)
- Cathrin Seibert
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, United Kingdom
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13
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Tzouros M, Pähler A. A Targeted Proteomics Approach to the Identification of Peptides Modified by Reactive Metabolites. Chem Res Toxicol 2009; 22:853-62. [DOI: 10.1021/tx800426x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Manuel Tzouros
- Drug Metabolism and Pharmacokinetics, Non-Clinical Safety, Pharmaceuticals Division, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Axel Pähler
- Drug Metabolism and Pharmacokinetics, Non-Clinical Safety, Pharmaceuticals Division, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
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14
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Lisitsa AV, Petushkova NA, Nikitin IP, Zgoda VG, Karuzina II, Moshkovskii SA, Larina OV, Skipenko OG, Polyschuk LO, Thiele H, Archakov AI. One-dimensional proteomic mapping of human liver cytochromes P450. BIOCHEMISTRY (MOSCOW) 2009; 74:153-61. [DOI: 10.1134/s0006297909020059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Dail MB, Shack LA, Chambers JE, Burgess SC. Global liver proteomics of rats exposed for 5 days to phenobarbital identifies changes associated with cancer and with CYP metabolism. Toxicol Sci 2008; 106:556-69. [PMID: 18796496 PMCID: PMC2581678 DOI: 10.1093/toxsci/kfn198] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 09/10/2008] [Indexed: 12/14/2022] Open
Abstract
A global proteomics approach was applied to model the hepatic response elicited by the toxicologically well-characterized xenobiotic phenobarbital (PB), a prototypical inducer of hepatic xenobiotic metabolizing enzymes and a well-known nongenotoxic liver carcinogen in rats. Differential detergent fractionation two-dimensional liquid chromatography electrospray ionization tandem mass spectrometry and systems biology modeling were used to identify alterations in toxicologically relevant hepatic molecular functions and biological processes in the livers of rats following a 5-day exposure to PB at 80 mg/kg/day or a vehicle control. Of the 3342 proteins identified, expression of 121 (3.6% of the total proteins) was significantly increased and 127 (3.8%) significantly decreased in the PB group compared to controls. The greatest increase was seen for cytochrome P450 (CYP) 2B2 (167-fold). All proteins with statistically significant differences from control were then analyzed using both Gene Ontology (GO) and Ingenuity Pathways Analysis (IPA, 5.0 IPA-Tox) for cellular location, function, network connectivity, and possible disease processes, especially as they relate to CYP-mediated metabolism and nongenotoxic carcinogenesis mechanisms. The GO results suggested that PB's mechanism of nongenotoxic carcinogenesis involves both increased xenobiotic metabolism, especially induction of the 2B subfamily of CYP enzymes, and increased cell cycle activity. Apoptosis, however, also increased, perhaps, as an attempt to counter the rising cancer threat. Of the IPA-mapped proteins, 41 have functions which are procarcinogenic and 14 anticarcinogenic according to the hypothesized nongenotoxic mechanism of imbalance between apoptosis and cellular proliferation. Twenty-two additional IPA nodes can be classified as procarcinogenic by the competing theory of increased metabolism resulting in the formation of reactive oxygen species. Since the systems biology modeling corresponded well to PB effects previously elucidated via more traditional methods, the global proteomic approach is proposed as a new screening methodology that can be incorporated into future toxicological studies.
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Affiliation(s)
- Mary B. Dail
- Center for Environmental Health Sciences, College of Veterinary Medicine
- Department of Basic Sciences, College of Veterinary Medicine
| | - L. Allen Shack
- Department of Basic Sciences, College of Veterinary Medicine
| | - Janice E. Chambers
- Center for Environmental Health Sciences, College of Veterinary Medicine
- Department of Basic Sciences, College of Veterinary Medicine
| | - Shane C. Burgess
- Department of Basic Sciences, College of Veterinary Medicine
- Mississippi Agriculture and Forestry Experiment Station
- Institute for Digital Biology
- Life Sciences and Biotechnology Institute, Mississippi State University, Mississippi State, Mississippi 39762
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16
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Rezen T, Contreras JA, Rozman D. Functional Genomics Approaches to Studies of the Cytochrome P450 Superfamily. Drug Metab Rev 2008; 39:389-99. [PMID: 17786628 DOI: 10.1080/03602530701498760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Functional genomics approaches are widely implemented in current research and have found application in many areas of biology. This review will present research fields, novel findings and new tools developed in the cytochrome P450 field using the functional genomics techniques. The most widely used method is microarray technology, which has already greatly contributed to the understanding of the cytochromes P450 function and expression. Several focused CYP microarrays have been developed for genotyping, toxicogenomics and studies of CYP function of many different organisms. Our contribution to the CYP field by development of Steroltalk microarrays to study the cross-talk of cholesterol homeostasis and drug metabolism is also presented.
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Affiliation(s)
- Tadeja Rezen
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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17
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Redlich G, Zanger UM, Riedmaier S, Bache N, Giessing ABM, Eisenacher M, Stephan C, Meyer HE, Jensen ON, Marcus K. Distinction between human cytochrome P450 (CYP) isoforms and identification of new phosphorylation sites by mass spectrometry. J Proteome Res 2008; 7:4678-88. [PMID: 18828626 DOI: 10.1021/pr800231w] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In mammals, Cytochrome P450 (CYP) enzymes are bound to membranes of the endoplasmic reticulum and mitochondria, where they are responsible for the oxidative metabolism of many xenobiotics as well as organic endogenous compounds. In humans, 57 isoforms were identified which are classified based on sequence homology. In the present work, we demonstrate the performance of a mass spectrometry-based strategy to simultaneously detect and differentiate distinct human Cytochrome P450 (CYP) isoforms including the highly similar CYP3A4, CYP3A5, CYP3A7, as well as CYP2C8, CYP2C9, CYP2C18, CYP2C19, and CYP4F2, CYP4F3, CYP4F11, CYP4F12. Compared to commonly used immunodetection methods, mass spectrometry overcomes limitations such as low antibody specificity and offers high multiplexing possibilities. Furthermore, CYP phosphorylation, which may affect various biochemical and enzymatic properties of these enzymes, is still poorly analyzed, especially in human tissues. Using titanium dioxide resin combined with tandem mass spectrometry for phosphopeptide enrichment and sequencing, we discovered eight human P450 phosphorylation sites, seven of which were novel. The data from surgical human liver samples establish that the isoforms CYP1A2, CYP2A6, CYP2B6, CYP2E1, CYP2C8, CYP2D6, CYP3A4, CYP3A7, and CYP8B1 are phosphorylated in vivo. These results will aid in further investigation of the functional significance of protein phosphorylation for this important group of enzymes.
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Affiliation(s)
- Gorden Redlich
- Functional Proteomics, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, Universitaetsstr. 150, ZKF, D-44801 Bochum, Germany.
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18
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Getie-Kebtie M, Franke P, Aksamit R, Alterman MA. Experimental Evaluation of Protein Identification by an LC/MALDI/On-Target Digestion Approach. J Proteome Res 2008; 7:3697-707. [DOI: 10.1021/pr800258k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Melkamu Getie-Kebtie
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 29A, Room 2D12, 8800 Rockville Pike, Bethesda, Maryland 20892
| | - Peter Franke
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 29A, Room 2D12, 8800 Rockville Pike, Bethesda, Maryland 20892
| | - Robert Aksamit
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 29A, Room 2D12, 8800 Rockville Pike, Bethesda, Maryland 20892
| | - Michail A. Alterman
- Tumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Building 29A, Room 2D12, 8800 Rockville Pike, Bethesda, Maryland 20892
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19
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Lane CS, Wang Y, Betts R, Griffiths WJ, Patterson LH. Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling. Mol Cell Proteomics 2007; 6:953-62. [PMID: 17296599 PMCID: PMC2315784 DOI: 10.1074/mcp.m600296-mcp200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Quantitative changes in cytochrome P450 (CYP) proteins involved in drug metabolism as a consequence of drug treatment are important parameters in predicting the fates and pharmacological consequences of xenobiotics and drugs. In this study we undertook comparative P450 proteomics using liver from control and 1,4-bis-2-(3,5-dichloropyridyloxybenzene) (TCPOBOP)-dosed mice. The method involved separation of microsomal proteins by SDS-PAGE, trypsin digestion, and postdigest 18O/16O labeling followed by nano-LC-MS/MS for peptide identification and LC-MS for relative quantification. Seventeen P450 proteins were identified from mouse liver of which 16 yielded data sufficient for relative quantification. All the P450s detected were unambiguously identified except the highly homologous CYP2A4/2A5. With the exception of CYP2A12, -2D10, and -2F2, the levels of all the P450s quantified were affected by treatment with TCPOBOP (3 mg/kg). CYP1A2, -2A4/5, -2B10, -2B20, -2C29, -2C37, -2C38, -3A11, and -39A1 were up-regulated, and CYP2C40, -2E1, -3A41, and -27A1 down-regulated. The response of CYP2B20 to stimulation has not been distinguished previously from that of CYP2B10 because of the poor discrimination between these two proteins (they share 87% sequence identity). Differential response to chemical stimulation by closely related members of the CYP2C subfamily was also observed.
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Affiliation(s)
- Catherine S Lane
- The School of Pharmacy, University of London, London WC1N 1AX, United Kingdom
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20
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Wang Y, Al-Gazzar A, Seibert C, Sharif A, Lane C, Griffiths WJ. Proteomic analysis of cytochromes P450: a mass spectrometry approach. Biochem Soc Trans 2006; 34:1246-51. [PMID: 17073795 DOI: 10.1042/bst0341246] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In human, the CYP (cytochrome P450) superfamily comprises 57 genes arranged in 18 families and 42 subfamiles. These genes encode for enzymes involved in the metabolism of drugs, foreign chemicals, fatty acids, eicosanoids and cholesterol. Additionally, they play roles in bile acid biosynthesis, steroid synthesis and metabolism, and vitamin D3 synthesis and metabolism. Mutations in many CYP genes cause inborn errors of metabolism and contribute to increased risk of cancer. MS provides a convenient method for the identification and quantification of CYP enzymes, and in the present paper we will review the current state of the technology for such an analysis.
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Affiliation(s)
- Y Wang
- The School of Pharmacy, University of London, 29-39 Brunswick Square, London WC1N 1AX, UK
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21
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Zgoda V, Tikhonova O, Viglinskaya A, Serebriakova M, Lisitsa A, Archakov A. Proteomic profiles of induced hepatotoxicity at the subcellular level. Proteomics 2006; 6:4662-70. [PMID: 16897686 DOI: 10.1002/pmic.200600342] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the present study proteomes of liver samples were analyzed after administration of phenobarbital (PB) or 3-methylcholantrene (3-MC) to mice. Liver cell homogenates were subfractionated by differential ultracentrifugation into cytosol and microsomes, which were subjected to 2-DE to generate the proteomic maps of these fractions. 2-DE yielded 1100 and 800 protein spots for microsomes and cytosol, respectively. General trends of the fraction-specific alterations after 3-MC or PB treatment were evaluated using the Student's t-test and the principal component analysis (PCA). According to the PCA-derived data, the microsomal changes after 3-MC and PB treatment were quite similar. However, in the case of the cytosol data, the specificities of 3-MC- and PB-induced responses could be clearly distinguished from each other. Protein spots, whose expression levels differed from control, were identified by MALDI-TOF PMF. Proteomic studies such as those reported herein can be useful in identifying the molecular-based toxicity of lead drug candidates.
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Affiliation(s)
- Victor Zgoda
- V.N. Orekhovich Institute of Biomedical Chemistry RAMS, Moscow, Russia.
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22
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Shumyantseva VV, Bulko TV, Samenkova NF, Kuznetsova GP, Usanov SA, Schulze H, Bachmann TT, Schmid RD, Archakov AI. A new format of electrodes for the electrochemical reduction of cytochromes P450. J Inorg Biochem 2006; 100:1353-7. [PMID: 16697466 DOI: 10.1016/j.jinorgbio.2006.03.007] [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] [Received: 09/23/2005] [Revised: 03/20/2006] [Accepted: 03/21/2006] [Indexed: 01/25/2023]
Abstract
New approach to the electrochemical reduction of cytochromes P450 (P450s, CYPs) at electrodes chemically modified with appropriate substrates for P450s ("reverse" electrodes) was proposed. The method is based on the analysis of cyclic voltammograms, square-wave voltammograms and amperograms with subsequent determination of electrochemical characteristics such as catalytic current and redox potential. The sensitivity of proposed method is 0.2-1 nmol P450/electrode. The changes of maximal current and of redox potentials in square-wave voltammograms as well as the changes of catalytic current in amperometric experiments proved to be informative and reliable. Planar regime of screen-printed electrodes (strip-type sensors) enabled to utilise 20-60 microl of electrolyte volume. The enzyme-substrate pairs P450 2B4/benzphetamine and P450scc/cholesterol were investigated. Electrochemical parameters of electrodes with unspecific P450 substrates differed considerably from electrodes with appropriate substrates.
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Affiliation(s)
- Victoria V Shumyantseva
- Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, Pogodinskaya Street, 10, Moscow 119121, Russia.
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23
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Alterman MA, Kornilayev B, Duzhak T, Yakovlev D. QUANTITATIVE ANALYSIS OF CYTOCHROME P450 ISOZYMES BY MEANS OF UNIQUE ISOZYME-SPECIFIC TRYPTIC PEPTIDES: A PROTEOMIC APPROACH. Drug Metab Dispos 2005; 33:1399-407. [PMID: 15951447 DOI: 10.1124/dmd.105.004812] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A novel matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry method has been developed to quantitate cytochrome P450 (P450) isozymes based on their unique isozyme-specific tryptic peptides. It was shown that the molar ratio of P450 isozyme-specific peptides is linearly proportional to the mass peak area ratio of corresponding peptides not only in simple two-peptide mixtures, but also in complex digest mixtures. This approach is applicable both to in-gel (as shown for CYP2B1 and CYP2B2) and in-solution digests (as shown for CYP1A2, CYP2E1, and CYP2C19) and does not require introduction of stable isotopes or labeling with isotope-coded affinity tagging. The relative and absolute quantitation can be performed after developing corresponding calibration curves with synthesized P450 isozyme-specific peptide standards. The absolute quantitation of human P450 isozymes was performed by using CYP2B2 isozyme-specific peptide (1306.7 Da) as the universal internal standard. The utility of this approach was demonstrated for two highly homologous (>97%) rat liver CYP2B1 and CYP2B2 and three human P450 isozymes belonging to two different families and three different subfamilies: CYP1A2, CYP2E1, and CYP2C19. In summary, we have demonstrated that MALDI TOF-based peptide mass fingerprinting of different cytochrome P450 isozymes can provide not only qualitative but quantitative data, too.
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Affiliation(s)
- Michail A Alterman
- Biochemical Research Service Laboratory/Analytical Proteomics Laboratory, University of Kansas, Lawrence, KS 66047-3761, USA.
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Lane CS, Nisar S, Griffiths WJ, Fuller BJ, Davidson BR, Hewes J, Welham KJ, Patterson LH. Identification of cytochrome P450 enzymes in human colorectal metastases and the surrounding liver: a proteomic approach. Eur J Cancer 2004; 40:2127-34. [PMID: 15341988 DOI: 10.1016/j.ejca.2004.04.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2004] [Revised: 04/23/2004] [Accepted: 04/30/2004] [Indexed: 11/20/2022]
Abstract
We describe the direct identification of multiple cytochrome P450 (CYP) enzymes in healthy and cancerous tissue. CYPs in human liver colorectal metastases were compared with those in the surrounding liver using a mass spectrometry-based proteomic approach. Nano-scale reversed phase liquid chromatography combined with electrospray ionisation tandem mass spectrometry has been used to identify CYPs with no pre-selection of the proteins anticipated. Fourteen distinct CYP enzymes from the subfamilies 1A, 2A, 2B, 2C, 2D, 2E, 3A, 4A, 4F, 8B and 27A were positively identified; 13 in the liver samples and 12 in the tumour tissue. It was found that three of the colorectal metastases expressed essentially the same drug-metabolising pattern of CYPs as the surrounding liver, whilst three tumour samples from different individuals showed no CYP expression. This was likely in at least one case to be due to low sample mass. The CYP expression profile in an individual tumour is likely to be an important determinant in predicting the outcome of cancer chemotherapy.
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Affiliation(s)
- C S Lane
- Department of Pharmaceutical and Biological Chemistry, The School of Pharmacy, University of London, 29/39 Brunswick Square, WC1N 1AX, UK
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