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What if? Mouse proteomics after gene inactivation. J Proteomics 2019; 199:102-122. [DOI: 10.1016/j.jprot.2019.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 03/09/2019] [Accepted: 03/10/2019] [Indexed: 12/17/2022]
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2
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Serum protein changes in a rat model of chronic pain show a correlation between animal and humans. Sci Rep 2017; 7:41723. [PMID: 28145509 PMCID: PMC5286399 DOI: 10.1038/srep41723] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/03/2017] [Indexed: 01/02/2023] Open
Abstract
In previous works we showed the overexpression of some proteins in biological fluids from patients suffering chronic pain. In this proteomic study we analysed serum from a rat model of neuropathic pain obtained by the chronic constriction injury (CCI) of sciatic nerve, at two time intervals, 2 and 5 weeks after the insult, to find proteins involved in the expression or mediation of pain. Sham-operated and CCI rats were treated with saline or indomethacin. Two weeks after ligation, we identified three serum proteins overexpressed in CCI rats, two of which, alpha-1-macroglobulin and vitamin D-binding protein (VDBP), remained increased 5 weeks post-surgery; at this time interval, we found increased levels of further proteins, namely apolipoprotein A-I (APOA1), apolipoprotein E (APOE), prostaglandin-H2 D-isomerase (PTGDS) and transthyretin (TTR), that overlap the overexpressed proteins found in humans. Indomethacin treatment reversed the effects of ligation. The qPCR analysis showed that transcript levels of APOA1, APOE, PTGDS and VDBP were overexpressed in the lumbar spinal cord (origin of sciatic nerve), but not in the striatum (an unrelated brain region), of CCI rats treated with saline 5 weeks after surgery, demonstrating that the lumbar spinal cord is a possible source of these proteins.
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Christensen BO, Overgaard J, Vorum H, Honore B, Damsgaard TE. A proteomic analysis of the effect of radiation therapy on wound healing in women reconstructed with the TRAM flap. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.411134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Gianazza E, Sensi C, Eberini I, Gilardi F, Giudici M, Crestani M. Inflammatory serum proteome pattern in mice fed a high-fat diet. Amino Acids 2012; 44:1001-8. [PMID: 23224824 DOI: 10.1007/s00726-012-1433-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/17/2012] [Indexed: 02/01/2023]
Abstract
To investigate the influence of diet on serum protein pattern, mice were fed for 8 weeks either control chow or a high-fat diet (containing 21 % w/w milk fat and 0.2 % w/w cholesterol); sera were collected and analyzed by 2-DE. The main positive acute-phase reactant proteins, haptoglobin and hemopexin, were significantly up-regulated in animals receiving the high-fat diet. Data on all other proteins also pointed to an inflammatory condition in these animals. The largest change in concentration was observed for carboxylesterase N, a circulating enzyme seldom connected with lipid metabolism in earlier reports. These observations agree with the notion of a link between diet-induced hyperlipidemia and the inflammatory component of its cardiovascular sequels in humans, but the effects in the experimental animals are massive and obviously affect most of the major serum proteins.
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Affiliation(s)
- Elisabetta Gianazza
- Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, via G. Balzaretti 9, 20133 Milan, Italy.
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Gianazza E, Wait R, Eberini I, Sensi C, Sironi L, Miller I. Proteomics of rat biological fluids — The tenth anniversary update. J Proteomics 2012; 75:3113-28. [DOI: 10.1016/j.jprot.2012.03.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 03/26/2012] [Accepted: 03/28/2012] [Indexed: 01/29/2023]
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Gianazza E, Vegeto E, Eberini I, Sensi C, Miller I. Neglected markers: Altered serum proteome in murine models of disease. Proteomics 2012; 12:691-707. [DOI: 10.1002/pmic.201100320] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 08/28/2011] [Indexed: 11/09/2022]
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Gong Y, Chen N, Wang FQ, Wang ZH, Xu HX. Serum proteome alteration of severe sepsis in the treatment of continuous renal replacement therapy. Nephrol Dial Transplant 2009; 24:3108-14. [DOI: 10.1093/ndt/gfp231] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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van Steeg TJ, Krekels EHJ, Danhof M, de Lange ECM. Reproducible and time-dependent modification of serum protein binding in Wistar Kyoto rats. J Pharmacol Toxicol Methods 2007; 56:72-8. [PMID: 17376707 DOI: 10.1016/j.vascn.2007.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The theoretical basis of the influence of (alterations in) plasma protein binding on pharmacokinetics (PK) is well-established. In contrast, the impact of protein binding on pharmacodynamics has not been examined in a systematic manner. Here we present an experimental approach to modify serum protein levels and binding in the rat, in a robust, reproducible, and time-dependent manner. METHOD Male Wistar Kyoto rats were divided into three different groups. The control group (n=4) did not receive treatment. In the cannulation(-) group (n=6) the rats were instrumented with three permanent blood cannulas. The rats in the cannulation(+) group received in addition to the cannulation a subcutaneous injection of turpentine oil of 100 microl/100 g bodyweight. The effects were characterized in terms of 1) the time course of serum levels of albumin and alpha(1)-acid glycoprotein (AGP), and 2) the effect on the ex vivo serum protein binding of S(-)-propranolol. RESULTS In control rats the AGP serum concentration was stable at a value of 169+/-16 microg/ml. In the cannulation(-) group a maximum ten- to fifteen-fold increase in serum AGP concentration was observed at 48 h post surgery, followed by a gradual return back to baseline within 1 week. In the cannulation(+) group a similar concentration-time profile for AGP was found, but without a complete return to baseline within 1 week and with a much higher variability. Ex vivo, an increase in AGP serum concentration from 55 to 675 microg/ml resulted in a profound decrease in the free fraction of S(-)-propranolol from 14+/-0.6 to 1.9+/-0.3%. CONCLUSIONS In conclusion, through cannulation alone the serum protein levels and binding were modified in a robust, reproducible and time-dependent manner. Therefore this experimental approach is suitable for the investigation of the influence of protein binding on both pharmacokinetics and pharmacodynamics.
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Affiliation(s)
- Tamara J van Steeg
- Leiden Amsterdam Center for Drug Research, Leiden University, Division of Pharmacology, Leiden, The Netherlands
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10
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Komori N, Takemori N, Kim HK, Singh A, Hwang SH, Foreman RD, Chung K, Chung JM, Matsumoto H. Proteomics study of neuropathic and nonneuropathic dorsal root ganglia: altered protein regulation following segmental spinal nerve ligation injury. Physiol Genomics 2007; 29:215-30. [PMID: 17213366 DOI: 10.1152/physiolgenomics.00255.2006] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Peripheral nerve injury is often followed by the development of severe neuropathic pain. Nerve degeneration accompanied by inflammatory mediators is thought to play a role in generation of neuropathic pain. Neuronal cell death follows axonal degeneration, devastating a vast number of molecules in injured neurons and the neighboring cells. Because we have little understanding of the cellular and molecular mechanisms underlying neuronal cell death triggered by nerve injury, we conducted a proteomics study of rat 4th and 5th lumbar (L4 and L5) dorsal root ganglion (DRG) after L5 spinal nerve ligation. DRG proteins were displayed on two-dimensional gels and analyzed through quantitative densitometry, statistical validation of the quantitative data, and peptide mass fingerprinting for protein identification. Among approximately 1,300 protein spots detected on each gel, we discovered 67 proteins that were tightly regulated by nerve ligation. We find that the injury to primary sensory neurons turned on multiple cellular mechanisms critical for the structural and functional integrity of neurons and for the defense against oxidative damage. Our data indicate that the regulation of metabolic enzymes was carefully orchestrated to meet the altered energy requirement of the DRG cells. Our data also demonstrate that ligation of the L5 spinal nerve led to the upregulation in the L4 DRG of the proteins that are highly expressed in embryonic sensory neurons. To understand the molecular mechanisms underlying neuropathic pain, we need to comprehend such dynamic aspect of protein modulations that follow nerve injury.
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Affiliation(s)
- Naoka Komori
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73190, USA.
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11
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Kim SW, Hwang HJ, Cho EJ, Oh JY, Baek YM, Choi JW, Yun JW. Time-Dependent Plasma Protein Changes in Streptozotocin-Induced Diabetic Rats before and after Fungal Polysaccharide Treatments. J Proteome Res 2006; 5:2966-76. [PMID: 17081048 DOI: 10.1021/pr0602601] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous studies about protein modulation with chemically induced models of diabetes in animals have yielded conflicting results, in that many investigators have reported different regulation patterns for the same proteins. Therefore, it is reasonable to determine biomarkers for prognosis and diagnosis of diabetes with time profiling for the candidate proteins. In this regard, we examined the influence of hypoglycemic fungal polysaccharides (EPS) on the time-dependent plasma protein alterations in streptozotocin-induced diabetic rats. The 2-DE analysis of rat plasma demonstrated that about 50 proteins from about 900 visualized spots were found to be differentially regulated, of which 20 spots were identified as principal diabetes-associated proteins. The results of time profiling revealed that most of the identified proteins showed significant alterations in a time-dependent manner during 14 days, with notable trends. Nine out of the twenty proteins displayed very similar time profiles between normal healthy and EPS-treated diabetic rats. Interestingly, the altered profiles of several proteins by diabetes induction almost returned to control levels after EPS treatments. In particular, we found a clear distinction in differential expression of oxidative stress proteins (ceruloplasmin and transferrin) and lipid metabolism related proteins (Apo A-I, Apo A-IV, and Apo E) in the STZ-induced diabetic rats. The data presented here have identified and characterized the time-dependent changes in plasma proteins associated with EPS treatment in STZ-induced diabetic rats, thereby leading to the discovery of early-response and late-response biomarkers in diabetic and EPS-treated states.
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Affiliation(s)
- Sang Woo Kim
- Department of Biotechnology, and Department of Bioindustry, Daegu University, Kyungsan, Kyungbuk 712-714, Korea
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12
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Kim SW, Hwang HJ, Kim HM, Lee MC, Shik Lee M, Choi JW, Yun JW. Effect of fungal polysaccharides on the modulation of plasma proteins in streptozotocin-induced diabetic rats. Proteomics 2006; 6:5291-302. [PMID: 16947119 DOI: 10.1002/pmic.200500933] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To search out novel biomarkers for monitoring diabetes prognosis, we examined the effect of hypoglycemic fungal exopolysaccharides (EPS) on the differential levels of plasma proteins in streptozotocin-induced diabetic rats. The orally administrated EPS exhibited an excellent hypoglycemic effect, lowering the average plasma glucose level, and increasing insulin secretion in diabetic rats. The 2-DE analysis of rat plasma demonstrated that about 500 visualized spots were differentially regulated, of which 20 spots were identified as principal diabetes-associated proteins. The distinct effect of diabetes induction on the pattern of rat plasma proteins includes the down-regulation of albumin, apolipoprotein E (Apo E), alpha1-inhibitor-3, fetuin beta, Gc-globulin, hemopexin, vitronectin, and transthyretin (TTR) monomer, and the up-regulation of Apo A-I, Apo A-IV, ceruloplasmin, alpha1-antitrypsin, serine protease inhibitor III, and transferrin. Those protein levels were interestingly restored to those of healthy rats by EPS treatment, although the order of magnitude of the changes differed widely. Two proteins of interest showed distinct differential expression with opposite trends: TTR tetramer was significantly down-regulated and immunoglobulin (Ig) kappa light chain was significantly up-regulated upon diabetes induction, both of which were also normalized to those of healthy groups after EPS treatment.
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Affiliation(s)
- Sang Woo Kim
- Department of Biotechnology, Daegu University, Kyungsan, Kyungbuk, Korea
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Hsu LW, Goto S, Nakano T, Lai CY, Lin YC, Kao YH, Chen SH, Cheng YF, Jawan B, Chiu KW, Chen CL. Immunosuppressive activity of serum taken from a liver transplant recipient after withdrawal of immunosuppressants. Transpl Immunol 2006; 17:137-46. [PMID: 17306745 DOI: 10.1016/j.trim.2006.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/07/2006] [Indexed: 01/10/2023]
Abstract
In orthotopic liver transplantation (OLT), tolerance is induced in a certain combination of donors and a recipient in rats and, in some clinical cases, rejection has not occurred in OLT patients after weaning off immunosuppression. However, this mechanism has not yet been elucidated. Among our cases of liver transplantation (LTx), one OLT patient (Patient A) has not required immunosuppressive drugs for the last 5 years, following post-transplant lymphoproliferative disease (PTLD). This patient's serum interleukin-2 levels were undetectable following withdrawal of immunosuppressants. The same serum taken after discontinuing the immunosuppressants inhibited concanavalin A blast cultured cells and up-regulated the IL-4/IFN-gamma gene expression ratio. These results suggested that other proteins were induced following withdrawal of immunosuppressants. Proteomic assay demonstrated 12 differentiated spots exclusive to this patient where immunosuppressants have been discontinued. Haptoglobin, found to have immunosuppressive activity in vitro, may play an important role in the maintenance of drug-free tolerance as a natural immunological suppressor after cessation of immunosuppression. Proteomic analysis will allow us to develop a novel weaning protocol for patients on long-term immunosuppression to avoid major immunosuppressant-related complications.
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Affiliation(s)
- Li-Wen Hsu
- Liver Transplantation Program and Department of Surgery, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Kaohsiung, Taiwan
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Lee YS, Chen PW, Tsai PJ, Su SH, Liao PC. Proteomics analysis revealed changes in rat bronchoalveolar lavage fluid proteins associated with oil mist exposure. Proteomics 2006; 6:2236-50. [PMID: 16518868 DOI: 10.1002/pmic.200500347] [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: 01/15/2023]
Abstract
Exposure to oil mist has been associated with a variety of acute and chronic respiratory effects. Using proteomics approaches to investigate exposure-associated proteins may provide useful information to understand the mechanisms of associated respiratory effects. The aim of this study was to investigate changes in rat bronchoalveolar lavage fluid proteins associated with oil mist exposure using nano-HPLC-ESI-MS/MS. The results revealed that 29 proteins exhibited significant changes after exposure. These proteins included surfactant-associated proteins (SP-A and SP-D), inflammatory proteins (complement component 3, immunoglobulins, lysozyme, etc.), growth factors (e.g., transforming growth factor alpha (TGF-alpha)), calcium-binding proteins (calcyclin, calgranulin A, calreticulin, and calvasculin), and other proteins (e.g., cathepsin D, saposin, and intestinal trefoil factor). To further evaluate changes in protein levels, a simple quantitative strategy was developed in this study. A large decrease in protein levels of SP-A and SP-D (0.24- and 0.38-fold, respectively) following exposure was observed. In contrast, protein levels of TGF-alpha and calcium-binding proteins were significantly increased (4.46- and 1.4-1.8-fold, respectively). Due to the diverse functions of these proteins, the results might contribute to understand the mechanisms involved in lung disorders induced by oil mist exposure.
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Affiliation(s)
- Yung-Shan Lee
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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15
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Duan X, Yarmush D, Berthiaume F, Jayaraman A, Yarmush ML. Immunodepletion of albumin for two-dimensional gel detection of new mouse acute-phase protein and other plasma proteins. Proteomics 2006; 5:3991-4000. [PMID: 16130172 DOI: 10.1002/pmic.200401257] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Immunodepletion of albumin to improve the 2-D gel resolution of human plasma proteins has recently been described. With the importance of mouse models in many studies in which serum or plasma is often analyzed, we have adopted this approach to immunoprecipitate mouse albumin and evaluated its effectiveness for 2-D separation of mouse plasma proteins. Purified polyclonal antibodies against mouse albumin were effective depleting intact albumin as well as its numerous fragments from mouse plasma samples. Removal of albumin resulted in better resolution of mouse plasma proteins. Three proteins, alpha2-macroglobulin, coagulation factor XII, and hemopexin, that were previously either undetectable or poorly resolved, were identified from albumin-depleted 2-D gels by peptide mass fingerprinting. Albumin depletion also led to partial loss of several other proteins such as clusterin and gelsolin. This loss can be attributed to the interaction with albumin itself because the specificity of the antibody was demonstrated by Western blot. When applying this method to the 2-D separation of plasma from inflamed mouse induced by cutaneous burn injury with superimposed Pseudomonas aeruginosa infection, the upregulation of inter alpha-trypsin inhibitor heavy chain 4 (ITIH4) and hemopexin was unambiguously detected along with other mouse acute-phase proteins (APP), including haptoglobin and serum amyloid A. Based on the significant increase of ITIH4, we propose that this protein is a new member of mouse APP that are upregulated during the inflammatory response.
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Affiliation(s)
- Xunbao Duan
- Center for Engineering in Medicine/Department of Surgery, Massachusetts General Hospital, Harvard Medical School and Shriners Burns Hospital, Boston, MA, USA
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He P, He HZ, Dai J, Wang Y, Sheng QH, Zhou LP, Zhang ZS, Sun YL, Liu F, Wang K, Zhang JS, Wang HX, Song ZM, Zhang HR, Zeng R, Zhao X. The human plasma proteome: analysis of Chinese serum using shotgun strategy. Proteomics 2005; 5:3442-53. [PMID: 16047309 DOI: 10.1002/pmic.200401301] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have investigated the serum proteome of Han-nationality Chinese by using shotgun strategy. A complete proteomics analysis was performed on two reference specimens from a total of 20 healthy donors, in which each sample was made from ten-pooled male or female serum, respectively. The methodology used encompassed (1) removal of six high-abundant proteins; (2) tryptic digestion of low- and high-abundant proteins of serum; (3) separation of peptide mixture by RP-HPLC followed by ESI-MS/MS identification. A total of 944 nonredundant proteins were identified under a stringent filter condition (X(corr) > or = 1.9, > or = 2.2, and > or = 3.75, < or = C(n) > or = 0.1, and R(sp) > or = 4.0) in both pooled male and female samples, in which 594 and 622 entire proteins were found, respectively. Compared with the total 3020 protein identifications confirmed by more than one laboratory or more than one specimen in HUPO Plasma Proteome Project (PPP) participating laboratories recently, 206 proteins were identified with at least two distinct peptides per protein and 185 proteins were considered as high-confidence identification. Moreover, some lower abundance serum proteins (ng/mL range) were detected, such as complement C5 and CA125, routinely used as an ovarian cancer marker in plasma and serum. The resulting nonredundant list of serum proteins would add significant information to the knowledge base of human plasma proteome and facilitate disease markers discovery.
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Affiliation(s)
- Ping He
- National Laboratory of Molecular Oncology, Cancer Institute & Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
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17
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Navarro MA, Carpintero R, Acín S, Arbonés-Mainar JM, Calleja L, Carnicer R, Surra JC, Guzmán-García MA, González-Ramón N, Iturralde M, Lampreave F, Piñeiro A, Osada J. Immune-regulation of the apolipoprotein A-I/C-III/A-IV gene cluster in experimental inflammation. Cytokine 2005; 31:52-63. [PMID: 15878672 DOI: 10.1016/j.cyto.2005.03.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2004] [Revised: 03/04/2005] [Accepted: 03/23/2005] [Indexed: 01/26/2023]
Abstract
Apolipoprotein A-IV is a member of the apo A-I/C-III/A-IV gene cluster. In order to investigate its hypothetical coordinated regulation, an acute phase was induced in pigs by turpentine oil injection. The hepatic expression of the gene cluster as well as the plasma levels of apolipoproteins were monitored at different time periods. Furthermore, the involvement of the inflammatory mediators' interleukins 1 and 6 and tumor necrosis factor in the regulation of this gene cluster was tested in cultured pig hepatocytes, incubated with those mediators and apo A-I/C-III/A-IV gene cluster expression at the mRNA level was measured. In response to turpentine oil-induced inflammation, a decreased hepatic apo A-IV mRNA expression was observed (independent of apo A-I and apo C-III mRNA) not correlating with the plasma protein levels. The distribution of plasma apo A-IV experienced a shift from HDL to larger particles. In contrast, the changes in apo A-I and apo C-III mRNA were reflected in their corresponding plasma levels. Addition of cytokines to cultured pig hepatocytes also decreased apo A-IV and apo A-I mRNA levels. All these results show that the down-regulation of apolipoprotein A-I and A-IV messages in the liver may be mediated by interleukin 6 and TNF-alpha. The well-known HDL decrease found in many different acute-phase responses also appears in the pig due to the decreased expression of apolipoprotein A-I and the enlargement of the apolipoprotein A-IV-containing HDL.
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Affiliation(s)
- María A Navarro
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Facultad de Veterinaria, Universidad de Zaragoza, Miguel Servet 177, E-50013 Zaragoza, Spain
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18
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Boots AM, Verhaert PD, te Poele RJ, Evers S, Coenen-de Roo CJ, Cleven J, Bos ES. Antigens up the nose: identification of putative biomarkers for nasal tolerance induction functional studies combined with proteomics. J Proteome Res 2005; 3:1056-62. [PMID: 15473695 DOI: 10.1021/pr049907c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Intranasal autoantigen delivery is the most effective means of inducing mucosal tolerance and suppression of autoimmune disease. In an effort to identify markers of the "tolerant state", we employed proteomics technology at the level of the cervical lymph node. The analysis revealed that nasal antigen administration (without adiuvant) led to modulation of various proteins among which the most prominent were haptoglobin, nonintegrin 67 kDa laminin receptor, and MRP8. The immunoregulatory haptoglobin may qualify as (bio)marker for effective immunotherapy.
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MESH Headings
- Adipokines
- Animals
- Antigen Presentation/immunology
- Biomarkers/analysis
- Biomarkers/metabolism
- Calgranulin A/analysis
- Calgranulin A/metabolism
- Carrier Proteins/analysis
- Carrier Proteins/metabolism
- Cell Line
- Chitinase-3-Like Protein 1
- Cytokines/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Down-Regulation/immunology
- Electrophoresis, Gel, Two-Dimensional
- Glycoproteins/immunology
- Haptoglobins/analysis
- Haptoglobins/metabolism
- Immune Tolerance/immunology
- Immunization
- Lectins
- Lymph Nodes/chemistry
- Lymph Nodes/cytology
- Lymph Nodes/immunology
- Lymphocyte Activation/immunology
- Mass Spectrometry
- Mice
- Mice, Inbred BALB C
- Mice, Knockout
- Mice, Transgenic
- Nasal Mucosa/immunology
- Ovalbumin/immunology
- Peptide Fragments/immunology
- Protein Transport/immunology
- Proteomics
- RNA-Binding Proteins
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Laminin/analysis
- Receptors, Laminin/metabolism
- Spleen/cytology
- Spleen/immunology
- T-Lymphocytes/immunology
- Up-Regulation/immunology
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Affiliation(s)
- Annemieke M Boots
- Department of Target Discovery and Pharmacology at NV Organon, Oss, The Netherlands
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Lee HJ, Lee DY, Joo WA, Sul D, Lee E, Kim CW. Differential expression of proteins in rat plasma exposed to benzene. Proteomics 2004; 4:3498-504. [PMID: 15468289 DOI: 10.1002/pmic.200400996] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Benzene, a ubiquitous environmental contaminant, is an important solvent in the chemical industry and is also known as a constituent of petroleum. It has been reported that benzene is associated with hematotoxicity including leukemia in humans and cancer in laboratory animals. To study protein expression alterations in rat plasma exposed to benzene, rats were exposed to levels of 1, 10, 100 ppm benzine for 6 h/day and 5 d/week for 2 or 6 weeks. Two-dimensional gel electrophoresis of rat plasma was carried out, and approximately 1000 protein spots were detected on the gels. The 11 spots which showed significantly different expression were selected and identified with matrix-assisted laser desorption/ionization-time of flight-mass spectrometry. Analyzing the targeted 11 spots, there was no correlation between the 2 and 6 weeks benzene-inhaled groups on up-regulated proteins (zinc finger protein, and tristetraprolin) and on down-regulated proteins (cAMP-regulated guanine nucleotide exchange factor II, protein kinase and unknown protein). The overexpressed proteins (inhibitor of kappaB-like protein, GTP-binding protein rab14, T-cell receptor alpha chain, and somatostatin transactivating factor-1) were detected only in groups inhaling benzene for 6 weeks. Among them the expression level of T-cell receptor alpha chain was confirmed by Western blot.
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Affiliation(s)
- Hyun-Ju Lee
- Graduate School of Life Science and Biotechnology, Korea University, Seoul, Korea
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Adkins JN, Varnum SM, Auberry KJ, Moore RJ, Angell NH, Smith RD, Springer DL, Pounds JG. Toward a human blood serum proteome: analysis by multidimensional separation coupled with mass spectrometry. Mol Cell Proteomics 2002; 1:947-55. [PMID: 12543931 DOI: 10.1074/mcp.m200066-mcp200] [Citation(s) in RCA: 582] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Blood serum is a complex body fluid that contains various proteins ranging in concentration over at least 9 orders of magnitude. Using a combination of mass spectrometry technologies with improvements in sample preparation, we have performed a proteomic analysis with submilliliter quantities of serum and increased the measurable concentration range for proteins in blood serum beyond previous reports. We have detected 490 proteins in serum by on-line reversed-phase microcapillary liquid chromatography coupled with ion trap mass spectrometry. To perform this analysis, immunoglobulins were removed from serum using protein A/G, and the remaining proteins were digested with trypsin. Resulting peptides were separated by strong cation exchange chromatography into distinct fractions prior to analysis. This separation resulted in a 3-5-fold increase in the number of proteins detected in an individual serum sample. With this increase in the number of proteins identified we have detected some lower abundance serum proteins (ng/ml range) including human growth hormone, interleukin-12, and prostate-specific antigen. We also used SEQUEST to compare different protein databases with and without filtering. This comparison is plotted to allow for a quick visual assessment of different databases as a subjective measure of analytical quality. With this study, we have performed the most extensive analysis of serum proteins to date and laid the foundation for future refinements in the identification of novel protein biomarkers of disease.
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Affiliation(s)
- Joshua N Adkins
- Biological Sciences Department, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Gianazza E, Eberini I, Villa P, Fratelli M, Pinna C, Wait R, Gemeiner M, Miller I. Monitoring the effects of drug treatment in rat models of disease by serum protein analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 771:107-30. [PMID: 12015995 DOI: 10.1016/s0378-4347(01)00562-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this review we list from literature investigations on rat serum proteins using electrophoretic techniques in connection with drug testing. From our own research work, we provide annotated two-dimensional maps of rat serum proteins under control and experimental conditions. Emphasis is on species-specific components and on the effects of acute and chronic inflammation. We discuss our project of structural proteomics on rat serum as a minimally invasive approach to pharmacological investigation, and we outline a typical experimental plan for drug testing according to the above guidelines. We then report in detail on the results of our trials of anti-inflammatory drugs on adjuvant arthritis, an animal model of disease resembling in many aspects human rheumatoid arthritis. We demonstrate a correlation between biochemical parameters and therapeutic findings and outline the advantages of the chosen methodological approach, which proved also sensitive in revealing "side effects" of the test drugs. In an appendix we describe our experimental protocol when performing two-dimensional electrophoresis of rat serum.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche, Università degli Studi di Milano via Balzaretti 9, I-20133 Milan, Italy.
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Wait R, Gianazza E, Eberini I, Sironi L, Dunn MJ, Gemeiner M, Miller I. Proteins of rat serum, urine, and cerebrospinal fluid: VI. Further protein identifications and interstrain comparison. Electrophoresis 2001; 22:3043-52. [PMID: 11565799 DOI: 10.1002/1522-2683(200108)22:14<3043::aid-elps3043>3.0.co;2-m] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have investigated the biological fluids--serum, cerebrospinal fluid, and urine--of three strains of rats; the present data extend our database (also available on-line) and may be of interest for pharmacological and toxicological investigation. Specifically, we have defined reference maps of the major protein components in cerebrospinal fluid and urine. Compartment-specific isoforms were recognized for transferrin and transthyretin. Mass spectrometric data established the cleavage site of the signal peptide and identified the N-terminal blocking group of prostaglandin D synthase from rat cerebrospinal fluid. A previously undescribed member of the family of low molecular mass rat urinary proteins was characterized as containing a sequence similar, but not identical, to the N-terminal region of rat urinary protein-2 (RUP-2), and divergent from RUP-1.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blood Proteins/analysis
- Cerebrospinal Fluid Proteins/analysis
- Databases, Protein
- Electrophoresis, Gel, Two-Dimensional
- Female
- Genetic Variation
- Internet
- Male
- Molecular Sequence Data
- Molecular Weight
- Protein Isoforms/analysis
- Proteins/analysis
- Proteins/classification
- Proteinuria/urine
- Rats/blood
- Rats/cerebrospinal fluid
- Rats/metabolism
- Rats/urine
- Rats, Inbred Lew
- Rats, Inbred WKY
- Rats, Sprague-Dawley
- Species Specificity
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Urine/chemistry
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Affiliation(s)
- R Wait
- Kennedy Institute of Rheumatology Division, Imperial College School of Medicine, Hammersmith, London, UK
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Sironi L, Tremoli E, Miller I, Guerrini U, Calvio AM, Eberini I, Gemeiner M, Asdente M, Paoletti R, Gianazza E. Acute-phase proteins before cerebral ischemia in stroke-prone rats: identification by proteomics. Stroke 2001; 32:753-60. [PMID: 11239198 DOI: 10.1161/01.str.32.3.753] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND AND PURPOSE A high degree of proteinuria has been reported in stroke-prone spontaneously hypertensive rats (SHRSP). We studied the effect of salt loading on the detailed protein pattern of serum and urine in 3 rat strains: Wistar-Kyoto, spontaneously hypertensive rats, and SHRSP, an inbred animal model for a complex form of cerebrovascular disorder resembling the human disease. METHODS Rats were given a permissive diet and received 1% NaCl in drinking water. The protein pattern in body fluids was assessed over time by 2-dimensional electrophoretic analysis. Brain alterations were monitored by MRI and histology. RESULTS Several proteins were excreted in urine after weeks of treatment and in advance of stroke: transferrin, hemopexin, albumin, alpha(2)-HS-glycoprotein, kallikrein-binding protein, alpha(1)-antitrypsin, Gc-globulin, and transthyretin. Markers of an inflammatory response, including very high levels of thiostatin, were detected in the serum of SHRSP at least 4 weeks before a stroke occurred. CONCLUSIONS In SHRSP subjected to salt loading, an atypical inflammatory condition and widespread alterations of vascular permeability developed before the appearance of anomalous features in the brain detected by MRI. Urinary concentrations of each of the excreted serum proteins correlated positively with time before stroke occurred.
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Affiliation(s)
- L Sironi
- Dipartimento di Scienze Farmacologiche, Facoltà di Farmacia, Università degli Studi, Milan, Italy
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