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Huang L, Shao D, Wang Y, Cui X, Li Y, Chen Q, Cui J. Human body-fluid proteome: quantitative profiling and computational prediction. Brief Bioinform 2021; 22:315-333. [PMID: 32020158 PMCID: PMC7820883 DOI: 10.1093/bib/bbz160] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
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Affiliation(s)
- Lan Huang
- College of Computer Science and Technology in the Jilin University
| | - Dan Shao
- College of Computer Science and Technology in the Jilin University
- College of Computer Science and Technology in Changchun University
| | - Yan Wang
- College of Computer Science and Technology in the Jilin University
| | - Xueteng Cui
- College of Computer Science and Technology in the Changchun University
| | - Yufei Li
- College of Computer Science and Technology in the Changchun University
| | - Qian Chen
- College of Computer Science and Technology in the Jilin University
| | - Juan Cui
- Department of Computer Science and Engineering in the University of Nebraska-Lincoln
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Mahdavi P, Nojavan S, Asadi S. An investigation on the effect of filtration and dilution of biological samples on electromembrane extraction efficiency: Determination of basic drugs in plasma and urine samples. SEPARATION SCIENCE PLUS 2020. [DOI: 10.1002/sscp.202000058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Parisa Mahdavi
- Department of analytical chemistry and pollutants Shahid Beheshti University Tehran Tehran Iran
| | - Saeed Nojavan
- Department of analytical chemistry and pollutants Shahid Beheshti University Tehran Tehran Iran
| | - Sakine Asadi
- Department of analytical chemistry and pollutants Shahid Beheshti University Tehran Tehran Iran
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3
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Emissions of terbium metal-organic frameworks modulated by dispersive/agglomerated gold nanoparticles for the construction of prostate-specific antigen biosensor. Anal Bioanal Chem 2019; 411:3979-3988. [PMID: 31089787 DOI: 10.1007/s00216-019-01883-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
Abstract
Herein, a universal and multifunctional fluorescence sensor platform is designed by the interaction of aggregation/dispersion gold nanoparticles (AuNPs) with Tb-metal-organic frameworks (Tb-MOFs). It is found that the dispersed AuNPs rather than the aggregated ones can quench effectively the fluorescence of Tb-MOFs, and the quenching process presumably involves the mechanism of inner filter effect (IFE), dynamic quenching effect (DQE), and fluorescence resonance energy transfer (FRET). The different affinities of aptamer and aptamer-target complex toward AuNPs are employed to modulate the fluorescence signal change of Tb-MOFs. As the proof of concept, prostate-specific antigen (PSA), an efficient tumor indicator for prostate cancer, is selected as the target. At first, the PSA aptamer can protect AuNPs against salt-induced aggregation, leading to the fluorescence of Tb-MOFs quenching. Subsequently, upon PSA introduction, the rigid aptamer-PSA complex is formed and cannot stabilize AuNPs in high salt conditions, so the AuNPs aggregate significantly and the fluorescence of Tb-MOFs is restored. The linear range of PSA is achieved from 1 to 100 ng/mL with a detection limit of 0.36 ng/mL. Finally, this method has been validated to be sensitive and specific for PSA in human urine samples. Graphical abstract.
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Anania VG, Yu K, Pingitore F, Li Q, Rose CM, Liu P, Sandoval W, Herman AE, Lill JR, Mathews WR. Discovery and Qualification of Candidate Urinary Biomarkers of Disease Activity in Lupus Nephritis. J Proteome Res 2019; 18:1264-1277. [PMID: 30525646 DOI: 10.1021/acs.jproteome.8b00874] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lupus nephritis (LN) is a severe clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Assessment of severity and activity of renal involvement in SLE requires a kidney biopsy, an invasive procedure with limited prognostic value. Noninvasive biomarkers are needed to inform treatment decisions and to monitor disease activity. Proteinuria is associated with disease progression in LN; however, the composition of the LN urinary proteome remains incompletely characterized. To address this, we profiled LN urine samples using complementary mass spectrometry-based methods: protein gel fractionation, chemical labeling using tandem mass tags, and data-independent acquisition. Combining results from these approaches yielded quantitative information on 2573 unique proteins in urine from LN patients. A multiple-reaction monitoring (MRM) method was established to confirm eight proteins in an independent cohort of LN patients, and seven proteins (transferrin, α-2-macroglobulin, haptoglobin, afamin, α-1-antitrypsin, vimentin, and ceruloplasmin) were confirmed to be elevated in LN urine compared to healthy controls. In this study, we demonstrate that deep mass spectrometry profiling of a small number of patient samples can identify high-quality biomarkers that replicate in an independent LN disease cohort. These biomarkers are being used to inform clinical biomarker strategies to support longitudinal and interventional studies focused on evaluating disease progression and treatment efficacy of novel LN therapeutics.
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Sensitivity and specificity of 47 kDa polyclonal antibody for detection of bladder cancer cells in urine of hematuria patients. AFRICAN JOURNAL OF UROLOGY 2018. [DOI: 10.1016/j.afju.2018.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Vinaiphat A, Charngkaew K, Thongboonkerd V. More complete polarization of renal tubular epithelial cells by artificial urine. Cell Death Discov 2018; 4:47. [PMID: 30323952 PMCID: PMC6180081 DOI: 10.1038/s41420-018-0112-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 02/06/2023] Open
Abstract
Cell polarization using Transwell is a common method employed to study renal tubular epithelial cells. However, this conventional protocol does not precisely recapitulate renal tubular epithelial cell phenotypes. In this study, we simulated renal physiological microenvironment by replacing serum-containing culture medium in upper chamber of the Transwell with physiologic artificial urine (AU) (to mimic renal tubular fluid), whereas the lower chamber still contained serum-containing medium (to mimic plasma-enriched renal interstitium). Comparing to the conventional protocol (control), the AU-assisted protocol offered more complete polarization of MDCK renal tubular cells as indicated by higher transepithelial electrical resistance (TER) and greater levels of tight junction (TJ) proteins (ZO-1 and occludin). Transmission electron microscopy (TEM) showed greater densities of TJ and desmosome, narrower intercellular spaces, greater cell height, and longer microvilli in the AU-treated cells. Secretome analysis revealed that the AU-treated cells secreted greater proportion of the proteins matched to normal human urinary proteome via both classical and non-classical secretory pathways. Finally, modifying/omitting each component of AU (one at a time) followed by validation revealed that urea was responsible for such property of AU to improve cell polarization. These data indicate that replacing AU on the upper chamber of Transwell can improve or optimize renal cell polarization for more precise investigations of renal physiology and cell biology in vitro.
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Affiliation(s)
- Arada Vinaiphat
- 1Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,2Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komgrid Charngkaew
- 3Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Visith Thongboonkerd
- 1Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,4Center for Research in Complex Systems Science, Mahidol University, Bangkok, Thailand
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Lim J, Hwang S. Identification of Osteoporosis-Associated Protein Biomarkers from Ovariectomized Rat Urine. CURR PROTEOMICS 2017; 14:130-137. [PMID: 28579927 PMCID: PMC5427775 DOI: 10.2174/1570164614666161228124801] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 12/11/2022]
Abstract
Objective: Osteoporotic fracture is one of the most common health risks and aggravates the quality of life among postmenopausal women worldwide. In this study, osteoporosis-associated protein biomarkers were identified from urine of osteoporotic female Sprague-Dawley rats developed by ovariectomy. Method: Four months after the operation, the bone mineral density of the femur of ovariectomized rats was significantly lowered in comparison with that of the sham operated rats. The protein profiles of the urine samples collected from the sham, ovariectomized (OVX) and 2 month-old non-operated (Young) rats were compared by 2-D gel and MS spectrometry. Results: Proteins consistently expressed between Young and sham but differentially expressed in OVX rats were selected and identified. One down-regulated 21 kDa protein, superoxide dismutase (SOD), and 1 up-regulated 53-54 kDa protein, alph-1-antitrypsin (A1AT), were selected from urine of the ovariectomized rats by 2-D gel analysis. Further, a total of 30 with 19 up-regulated and 11-down-regulated proteins were selected by LC-MS analysis with more than 2-fold differences in spectral counts. The fact that SOD and A1AT are also listed in the 30 differential proteins suggests that our biomarker isolation procedure suitably represents osteoporosis-associated proteins in urine. Conclusion: Supporting the facts, the differential expressions of SOD and A1AT in urine could be validated by Western blotting. These urinary osteoporosis-associated proteins have high potentials to become candidates for non-invasive diagnosis of osteoporosis from urine.
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Affiliation(s)
- Jinkyu Lim
- Major in Food Biomaterials, Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, South Korea
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Zou L, Sun W. Human Urine Proteome: A Powerful Source for Clinical Research. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 845:31-42. [DOI: 10.1007/978-94-017-9523-4_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Lacroix C, Caubet C, Gonzalez-de-Peredo A, Breuil B, Bouyssié D, Stella A, Garrigues L, Le Gall C, Raevel A, Massoubre A, Klein J, Decramer S, Sabourdy F, Bandin F, Burlet-Schiltz O, Monsarrat B, Schanstra JP, Bascands JL. Label-free quantitative urinary proteomics identifies the arginase pathway as a new player in congenital obstructive nephropathy. Mol Cell Proteomics 2014; 13:3421-34. [PMID: 25205225 DOI: 10.1074/mcp.m114.040121] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Obstructive nephropathy is a frequently encountered situation in newborns. In previous studies, the urinary peptidome has been analyzed for the identification of clinically useful biomarkers of obstructive nephropathy. However, the urinary proteome has not been explored yet and should allow additional insight into the pathophysiology of the disease. We have analyzed the urinary proteome of newborns (n = 5/group) with obstructive nephropathy using label free quantitative nanoLC-MS/MS allowing the identification and quantification of 970 urinary proteins. We next focused on proteins exclusively regulated in severe obstructive nephropathy and identified Arginase 1 as a potential candidate molecule involved in the development of obstructive nephropathy, located at the crossroad of pro- and antifibrotic pathways. The reduced urinary abundance of Arginase 1 in obstructive nephropathy was verified in independent clinical samples using both Western blot and MRM analysis. These data were confirmed in situ in kidneys obtained from a mouse obstructive nephropathy model. In addition, we also observed increased expression of Arginase 2 and increased total arginase activity in obstructed mouse kidneys. mRNA expression analysis of the related arginase pathways indicated that the pro-fibrotic arginase-related pathway is activated during obstructive nephropathy. Taken together we have identified a new actor in the development of obstructive nephropathy in newborns using quantitative urinary proteomics and shown its involvement in an in vivo model of disease. The present study demonstrates the relevance of such a quantitative urinary proteomics approach with clinical samples for a better understanding of the pathophysiology and for the discovery of potential therapeutic targets.
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Affiliation(s)
- Chrystelle Lacroix
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Cécile Caubet
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Anne Gonzalez-de-Peredo
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Benjamin Breuil
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - David Bouyssié
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Alexandre Stella
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Luc Garrigues
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Caroline Le Gall
- ‖Methodomics, Toulouse, France; **Institut de Mathématiques de Toulouse, UMR 5219, INSA de Toulouse, Université de Toulouse, 135 Avenue de Rangueil, F-31077 Toulouse, France
| | - Anthony Raevel
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Angelique Massoubre
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Julie Klein
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
| | - Stéphane Decramer
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; ‡‡Nephrology and Internal Medicine Department, University Children's Hospital, Toulouse, France
| | - Frédérique Sabourdy
- §§Laboratoire de Biochimie Métabolique, IFB, CHU Purpan, and INSERM UMR 1037, CRCT CHU Rangueil, Toulouse, France
| | - Flavio Bandin
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; ‡‡Nephrology and Internal Medicine Department, University Children's Hospital, Toulouse, France
| | - Odile Burlet-Schiltz
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Bernard Monsarrat
- From the ‡Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, F-31077 Toulouse, France; §Université Paul Sabatier, Toulouse, France
| | - Joost-Peter Schanstra
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France;
| | - Jean-Loup Bascands
- §Université Paul Sabatier, Toulouse, France; ¶Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France;
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From hundreds to thousands: Widening the normal human Urinome (1). J Proteomics 2014; 112:53-62. [PMID: 25123350 DOI: 10.1016/j.jprot.2014.07.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
UNLABELLED It is currently unknown how many proteins can be detected in urine. Improving the analytical approach would increase their number and potentially strengthen their predictive potential in diseases. We developed a combination of analytical procedures for maximizing sensitivity and reproducibility of normal human urinary proteome analysis based on ultracentrifugation, vesicles separation, combinatorial peptide ligand libraries (CPLL) and solvent removal of pigments. Proteins were identified by an Orbitrap Velos Mass Spectrometry. Overall, 3429 proteins were characterized: most components (1615) were contained in vesicles while the remaining 1794 were equally distributed among CPLL and butanol insoluble fractions. Several proteins were detected exclusively in one of the phases of the procedure, suggesting that each step is crucial in the fractionation strategy. Many (1724) proteins are described here whose presence in urine has never been reported and represents a potential source of information considering that urine is the unique site of excretion of products of interaction of metabolic processes. Improving the characterization of normal urinary proteome would also represent the basis for the analysis of urine biomarkers in human diseases. BIOLOGICAL SIGNIFICANCE Sub-fractionating normal urine by successive steps (vesicle separation, CPLL and solvent treatments) allowed the identification of 3429 proteins, a relevant part (1724) being detected for the first time in urine. Several proteins of new description have been implicated in physiology pathways and in pathologies thus representing a potential source of new information on both metabolic processes and diseases.
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Rouillon J, Zocevic A, Leger T, Garcia C, Camadro JM, Udd B, Wong B, Servais L, Voit T, Svinartchouk F. Proteomics profiling of urine reveals specific titin fragments as biomarkers of Duchenne muscular dystrophy. Neuromuscul Disord 2014; 24:563-73. [DOI: 10.1016/j.nmd.2014.03.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/12/2014] [Accepted: 03/28/2014] [Indexed: 11/30/2022]
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12
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Mullen W. The human urinary proteome: combinational approaches to comprehensive mapping. Expert Rev Proteomics 2014; 9:375-7. [DOI: 10.1586/epr.12.36] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Zheng J, Liu L, Wang J, Jin Q. Urinary proteomic and non-prefractionation quantitative phosphoproteomic analysis during pregnancy and non-pregnancy. BMC Genomics 2013; 14:777. [PMID: 24215720 PMCID: PMC3832905 DOI: 10.1186/1471-2164-14-777] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 10/28/2013] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Progress in the fields of protein separation and identification technologies has accelerated research into biofluids proteomics for protein biomarker discovery. Urine has become an ideal and rich source of biomarkers in clinical proteomics. Here we performed a proteomic analysis of urine samples from pregnant and non-pregnant patients using gel electrophoresis and high-resolution mass spectrometry. Furthermore, we also apply a non-prefractionation quantitative phosphoproteomic approach using mTRAQ labeling to evaluate the expression of specific phosphoproteins during pregnancy comparison with non-pregnancy. RESULTS In total, 2579 proteins (10429 unique peptides) were identified, including 1408 from the urine of pregnant volunteers and 1985 from the urine of non-pregnant volunteers. One thousand and twenty-three proteins were not reported in previous studies at the proteome level and were unique to our study. Furthermore, we obtained 237 phosphopeptides, representing 105 phosphoproteins. Among these phosphoproteins, 16 of them were found to be significantly differentially expressed, of which 14 were up-regulated and two were down-regulated in urine samples from women just before vaginal delivery. CONCLUSION Taken together, these results offer a comprehensive urinary proteomic profile of healthy women during before and after vaginal delivery and novel information on the phosphoproteins that are differentially regulated during the maintenance of normal pregnancy. Our results may provide a better understanding of the mechanisms of pregnancy maintenance, potentially leading to the development of biomarker-based sensitive assays for understanding pregnancy.
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Affiliation(s)
| | | | | | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No,6, Rongjing East Street, BDA, Beijing 100176, China.
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Paramithiotis S, Grivokostopoulos N, Skandamis PN. Investigating the correlation of constitutive proteins with the growth limits of Salmonella enterica isolates from feeds in response to temperature, pH, formic and lactic acid. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Tyan YC, Yang MH, Chung TW, Lu CY, Tsai WC, Jong SB. Assessing human urinary proteome using a mass spectrometry-based profiling system combined with magnetic nanoparticles. Clin Chim Acta 2013; 420:54-61. [DOI: 10.1016/j.cca.2012.10.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2012] [Accepted: 10/10/2012] [Indexed: 01/11/2023]
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16
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Biodistribution and renal clearance of biocompatible lung targeted poly(ethylene glycol) (PEG) nanogel aggregates. J Control Release 2012; 164:65-73. [PMID: 23041417 DOI: 10.1016/j.jconrel.2012.09.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2012] [Accepted: 09/19/2012] [Indexed: 11/21/2022]
Abstract
A novel stabilized aggregated nanogel particle (SANP) drug delivery system was prepared for injectable passive lung targeting. Gel nanoparticles (GNPs) were synthesized by irreversibly cross-linking 8 Arm PEG thiol with 1,6-hexane-bis-vinylsulfone (HBVS) in phosphate buffer (PB, pH 7.4) containing 0.1% v/v Tween™ 80. Aggregated nanogel particles (ANPs) were generated by aggregating GNPs to micron-size, which were then stabilized (i.e., SANPs) using a PEG thiol polymer to prevent further growth-aggregation. The size of SANPs, ANPs and GNPs was analyzed using a Coulter counter and transmission electron microscopy (TEM). Stability studies of SANPs were performed at 37°C in rat plasma, phosphate buffered saline (PBS, pH 7.4) and PB (pH 7.4). SANPs were stable in rat plasma, PBS and PB over 7 days. SANPs were covalently labeled with HiLyte Fluor™ 750 (DYE-SANPs) to facilitate ex vivo imaging. Biodistribution of intravenous DYE-SANPs (30 μm, 4 mg in 500 μL PBS) in male Sprague-Dawley rats was compared to free HiLyte Fluor™ 750 DYE alone (1mg in 500 μL PBS) and determined using a Xenogen IVIS® 100 Imaging System. Biodistribution studies demonstrated that free DYE was rapidly eliminated from the body by renal filtration, whereas DYE-SANPs accumulated in the lung within 30 min and persisted for 48 h. DYE-SANPs were enzymatically degraded to their original principle components (i.e., DYE-PEG-thiol and PEG-VS polymer) and were then eliminated from the body by renal filtration. Histological evaluation using H & E staining and broncho alveolar lavage (BAL) confirmed that these flexible SANPs were not toxic. This suggests that because of their flexible and non-toxic nature, SANPs may be a useful alternative for treating pulmonary diseases such as asthma, pneumonia, tuberculosis and disseminated lung cancer.
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Starkey JM, Tilton RG. Proteomics and systems biology for understanding diabetic nephropathy. J Cardiovasc Transl Res 2012; 5:479-90. [PMID: 22581264 DOI: 10.1007/s12265-012-9372-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 05/01/2012] [Indexed: 01/07/2023]
Abstract
Like many diseases, diabetic nephropathy is defined in a histopathological context and studied using reductionist approaches that attempt to ameliorate structural changes. Novel technologies in mass spectrometry-based proteomics have the ability to provide a deeper understanding of the disease beyond classical histopathology, redefine the characteristics of the disease state, and identify novel approaches to reduce renal failure. The goal is to translate these new definitions into improved patient outcomes through diagnostic, prognostic, and therapeutic tools. Here, we review progress made in studying the proteomics of diabetic nephropathy and provide an introduction to the informatics tools used in the analysis of systems biology data, while pointing out statistical issues for consideration. Novel bioinformatics methods may increase biomarker identification, and other tools, including selective reaction monitoring, may hasten clinical validation.
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Affiliation(s)
- Jonathan M Starkey
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555-1060, USA
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Zerefos PG, Aivaliotis M, Baumann M, Vlahou A. Analysis of the urine proteome via a combination of multi-dimensional approaches. Proteomics 2012; 12:391-400. [DOI: 10.1002/pmic.201100212] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 10/06/2011] [Accepted: 11/26/2011] [Indexed: 11/06/2022]
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Molina L, Salvetat N, Ameur RB, Peres S, Sommerer N, Jarraya F, Ayadi H, Molina F, Granier C. Analysis of the variability of human normal urine by 2D-GE reveals a “public” and a “private” proteome. J Proteomics 2011; 75:70-80. [DOI: 10.1016/j.jprot.2011.06.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/22/2011] [Accepted: 06/25/2011] [Indexed: 01/30/2023]
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Yang MH, Chu PY, Chen SCJ, Chung TW, Chen WC, Tan LB, Kan WC, Wang HY, Su SB, Tyan YC. Characterization of ADAM28 as a biomarker of bladder transitional cell carcinomas by urinary proteome analysis. Biochem Biophys Res Commun 2011; 411:714-20. [PMID: 21782798 DOI: 10.1016/j.bbrc.2011.07.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2011] [Accepted: 07/07/2011] [Indexed: 01/13/2023]
Abstract
Human urine contains a large number of proteins and peptides (the urinary proteome). Global analysis of the human urinary proteome is important for understanding urinary tract diseases. Bladder cancer is the most common urological cancer with higher incidence rates in endemic areas of Blackfoot disease (BFD) in southern Taiwan. The aim of this study was to use the proteomic approach to establish urinary protein biomarkers of bladder cancer. ADAM28, identified by proteomic approaches and confirmed by Western blotting, showed significant differences compared with normal individuals, so it may be a biomarker of bladder cancer.
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Affiliation(s)
- Ming-Hui Yang
- Department of Chemical and Material Engineering, National Yulin University of Science and Technology, Taiwan
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21
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Marimuthu A, O’Meally RN, Chaerkady R, Subbannayya Y, Nanjappa V, Kumar P, Kelkar DS, Pinto SM, Sharma R, Renuse S, Goel R, Christopher R, Delanghe B, Cole RN, Harsha H, Pandey A. A comprehensive map of the human urinary proteome. J Proteome Res 2011; 10:2734-43. [PMID: 21500864 PMCID: PMC4213861 DOI: 10.1021/pr2003038] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The study of the human urinary proteome has the potential to offer significant insights into normal physiology as well as disease pathology. The information obtained from such studies could be applied to the diagnosis of various diseases. The high sensitivity, resolution, and mass accuracy of the latest generation of mass spectrometers provides an opportunity to accurately catalog the proteins present in human urine, including those present at low levels. To this end, we carried out a comprehensive analysis of human urinary proteome from healthy individuals using high-resolution Fourier transform mass spectrometry. Importantly, we used the Orbitrap for detecting ions in both MS (resolution 60 000) and MS/MS (resolution 15 000) modes. To increase the depth of our analysis, we characterized both unfractionated as well as lectin-enriched proteins in our experiments. In all, we identified 1,823 proteins with less than 1% false discovery rate, of which 671 proteins have not previously been reported as constituents of human urine. This data set should serve as a comprehensive reference list for future studies aimed at identification and characterization of urinary biomarkers for various diseases.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Manipal University, Manipal 576104, Karnataka, India
| | - Robert N. O’Meally
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Rajiv Gandhi University of Health Sciences, Bangalore 560041, Karnataka, India
| | - Vishalakshi Nanjappa
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Praveen Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Dhanashree S. Kelkar
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- School of Biotechnology, Amrita University, Kollam 690525, Kerala, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Rakesh Sharma
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560006, Karnataka, India
| | - Santosh Renuse
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- School of Biotechnology, Amrita University, Kollam 690525, Kerala, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Rita Christopher
- Department of Neurochemistry, National Institute of Mental Health and Neuro Sciences, Bangalore 560006, Karnataka, India
| | | | - Robert N. Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
| | - H.C. Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, United States
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22
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Siwy J, Mullen W, Golovko I, Franke J, Zürbig P. Human urinary peptide database for multiple disease biomarker discovery. Proteomics Clin Appl 2011; 5:367-74. [PMID: 21591268 DOI: 10.1002/prca.201000155] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/04/2011] [Accepted: 03/09/2011] [Indexed: 11/07/2022]
Abstract
PURPOSE Human urine is an ideal candidate for use in clinical diagnostics. It is easily available, as untrained personnel can collect it. It correlates well with the pathophysiology of a number of diseases, making it a useful source for clinical proteomics. EXPERIMENTAL DESIGN In this article, we give an update of the human urinary peptide database derived from over 13,000 data sets of CE-MS by now. RESULTS Urine samples from both patients and healthy subjects were analyzed by CE-MS; these included 47 different pathophysiological conditions. Besides defining biomarkers by their experimental parameters, information on their sequences provides fundamental data into the pathological pathways of diseases. Therefore, we have sequenced 953 urinary peptides by using state-of-the-art top-down MS/MS. Identified biomarkers of all clinical proteomic CE-MS studies including their regulation are also listed in this work. CONCLUSIONS AND CLINICAL RELEVANCE Biomarker discovery can be used in the management of a wide range of diseases, by combining these data sets of the database. Taking this approach, we can reveal details, at a molecular level, on the pathogenesis of a number of diseases, in particular those associated with urine production and excretion.
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Zürbig P, Dihazi H, Metzger J, Thongboonkerd V, Vlahou A. Urine proteomics in kidney and urogenital diseases: Moving towards clinical applications. Proteomics Clin Appl 2011; 5:256-68. [PMID: 21591267 DOI: 10.1002/prca.201000133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 03/04/2011] [Accepted: 03/09/2011] [Indexed: 12/14/2022]
Abstract
To date, multiple biomarker discovery studies in urine have been conducted. Nevertheless, the rate of progression of these biomarkers to qualification and even more clinical application is extremely low. The scope of this article is to provide an overview of main clinically relevant proteomic findings from urine focusing on kidney diseases, bladder and prostate cancers. In addition, approaches for promoting the use of urine in clinical proteomics including potential means to facilitate the validation of existing promising findings (biomarker candidates identified from previous studies) and to increase the chances for success for the identification of new biomarkers are discussed.
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24
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Lu CM, Wu YJ, Chen CC, Hsu JL, Chen JC, Chen JYF, Huang CH, Ko YC. Identification of low-abundance proteins via fractionation of the urine proteome with weak anion exchange chromatography. Proteome Sci 2011; 9:17. [PMID: 21473785 PMCID: PMC3079594 DOI: 10.1186/1477-5956-9-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 04/08/2011] [Indexed: 12/28/2022] Open
Abstract
Background Low-abundance proteins are difficultly observed on the two-dimensional gel electrophoresis (2-DE) maps of urine proteome, because they are usually obscured by high-abundance proteins such as albumin and immunoglobulin. In this study, a novel fractionation method was developed for enriching low-abundance proteins by removing high-abundance proteins and progressive elution with salts of various concentrations. Results Stepwise weak anion exchange (WAX) chromatography, which applied DEAE-Sephacel resin with non-fixed volume elution, was used to fractionate urine proteome prior to performing 2-DE. Urine proteome was separated into four fractions by progressively eluting the column with 0 M, 50 mM, 100 mM, and 1 M NaCl solutions. Most of the heavy and light immunoglobulin chains appeared in the eluent. After the high-abundance proteins were removed, various low-abundance proteins were enriched and could be easily identified. The potential of this method for obtaining diversified fractionations was demonstrated by eluting the column separately with Na2SO4 and MgCl2 solutions. The 2-DE maps of the fractions eluted with these different salt solutions of identical ionic strength revealed markedly different stain patterns. Conclusion The present study demonstrated that this fractionation method could be applied for purposes of enriching low-abundance proteins and obtaining diversified fractionations of urine, and potentially other proteomes.
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Affiliation(s)
- Chih-Ming Lu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Buddhist Da Lin Tzu Chi General Hospital, Chiayi, Taiwan
| | - Yu-Jen Wu
- Department of Beauty Science, Meiho University, Pingtung, Taiwan
| | - Cheng-Chi Chen
- Department of Beauty Science, Meiho University, Pingtung, Taiwan
| | - Jue-Liang Hsu
- Graduate Institute of Biotechnology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Jiing-Chuan Chen
- Department of Food Science and Nutrition, Meiho University, Pingtung, Taiwan
| | - Jeff Yi-Fu Chen
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Hsiung Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Urology, Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ying-Chin Ko
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Nagaraj N, Mann M. Quantitative Analysis of the Intra- and Inter-Individual Variability of the Normal Urinary Proteome. J Proteome Res 2011; 10:637-45. [DOI: 10.1021/pr100835s] [Citation(s) in RCA: 179] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Nagarjuna Nagaraj
- Department for Proteomics and Signal Transduction at the Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- Department for Proteomics and Signal Transduction at the Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Chen YT, Chen CL, Chen HW, Chung T, Wu CC, Chen CD, Hsu CW, Chen MC, Tsui KH, Chang PL, Chang YS, Yu JS. Discovery of novel bladder cancer biomarkers by comparative urine proteomics using iTRAQ technology. J Proteome Res 2010; 9:5803-15. [PMID: 20806971 DOI: 10.1021/pr100576x] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A urine sample preparation workflow for the iTRAQ (isobaric tag for relative and absolute quantitation) technique was established. The reproducibility of this platform was evaluated and applied to discover proteins with differential levels between pooled urine samples from nontumor controls and three bladder cancer patient subgroups with different grades/stages (a total of 14 controls and 23 cancer cases in two multiplex iTRAQ runs). Combining the results of two independent clinical sample sets, a total of 638 urine proteins were identified. Among them, 55 proteins consistently showed >2-fold differences in both sample sets. Western blot analyses of individual urine samples confirmed that the levels of apolipoprotein A-I (APOA1), apolipoprotein A-II, heparin cofactor 2 precursor and peroxiredoxin-2 were significantly elevated in bladder cancer urine specimens (n = 25-74). Finally, we quantified APOA1 in a number of urine samples using a commercial ELISA and confirmed again its potential value for diagnosis (n = 126, 94.6% sensitivity and 92.0% specificity at a cutoff value of 11.16 ng/mL) and early detection (n = 71, 83.8% sensitivity and 94.0% specificity). Collectively, our results provide the first iTRAQ-based quantitative profile of bladder cancer urine proteins and represent a valuable resource for the discovery of bladder cancer markers.
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Affiliation(s)
- Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Taiwan
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27
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Mischak H, Kolch W, Aivaliotis M, Bouyssié D, Court M, Dihazi H, Dihazi GH, Franke J, Garin J, Gonzalez de Peredo A, Iphöfer A, Jänsch L, Lacroix C, Makridakis M, Masselon C, Metzger J, Monsarrat B, Mrug M, Norling M, Novak J, Pich A, Pitt A, Bongcam-Rudloff E, Siwy J, Suzuki H, Thongboonkerd V, Wang LS, Zoidakis J, Zürbig P, Schanstra JP, Vlahou A. Comprehensive human urine standards for comparability and standardization in clinical proteome analysis. Proteomics Clin Appl 2010; 4:464-78. [PMID: 21137064 DOI: 10.1002/prca.200900189] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 11/20/2009] [Accepted: 12/26/2009] [Indexed: 11/07/2022]
Abstract
PURPOSE Urine proteomics is emerging as a powerful tool for biomarker discovery. The purpose of this study is the development of a well-characterized "real life" sample that can be used as reference standard in urine clinical proteomics studies. EXPERIMENTAL DESIGN We report on the generation of male and female urine samples that are extensively characterized by different platforms and methods (CE-MS, LC-MS, LC-MS/MS, 1-D gel analysis in combination with nano-LC MS/MS (using LTQ-FT ultra), and 2-DE-MS) for their proteome and peptidome. In several cases analysis involved a definition of the actual biochemical entities, i.e. proteins/peptides associated with molecular mass and detected PTMs and the relative abundance of these compounds. RESULTS The combination of different technologies allowed coverage of a wide mass range revealing the advantages and complementarities of the different technologies. Application of these samples in "inter-laboratory" and "inter-platform" data comparison is also demonstrated. CONCLUSIONS AND CLINICAL RELEVANCE These well-characterized urine samples are freely available upon request to enable data comparison especially in the context of biomarker discovery and validation studies. It is also expected that they will provide the basis for the comprehensive characterization of the urinary proteome.
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Affiliation(s)
- Harald Mischak
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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28
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Application of Preparative Electrophoresis for Clinical Proteomics in Urine: Is it Feasible? J Med Biochem 2009. [DOI: 10.2478/v10011-009-0027-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Application of Preparative Electrophoresis for Clinical Proteomics in Urine: Is it Feasible?Urine samples are easily attainable which makes them ideal substrates for biomarker research. Various techniques have been employed to unravel the urine proteome and identify disease biomarkers. Even though the presence of high abundance proteins in urine is not so pronounced as in the case of plasma, the presence of proteolytic products, many of which at low abundance, along with numerous frequently random chemical modifications, makes the analysis of urinary proteins challenging. To facilitate the detection of low abundance urinary proteins, in the study presented herein we applied two different electrophoretic techniques, preparative Lithium Dodecyl Sulfate (LDS)-PAGE in combination with 2-DE for urinary protein separation and enrichment. Our results indicate the effectiveness of this approach for the enrichment of low abundance and low molecular weight proteins and peptides in urine, and contribute towards the establishment of a urinary proteomic database. The application of this technique as a biomarker discovery tool faces several challenges: these include down-scaling of the technique, possible recompensation for the consequent expected decrease in protein resolution, by optimizing steps of the experimental workflow as well as getting a good understanding of the technical variability of the technique. Under these conditions, preparative electrophoresis can become an effective tool for clinical proteomics applications.
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Sigdel TK, Klassen RB, Sarwal MM. Interpreting the proteome and peptidome in transplantation. Adv Clin Chem 2009; 47:139-69. [PMID: 19634780 DOI: 10.1016/s0065-2423(09)47006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Publication of the human proteome has prompted efforts to develop high-throughput techniques that can catalogue and quantify proteins and peptides present in different tissue types. The field of proteomics aims to identify, quantify, analyze, and functionally define a large number of proteins in cellular processes in different disease states on a global scale. Peptidomics, a newer name in the -omics world, measures and identifies naturally occurring low molecular weight peptides, also providing an insight into enzymatic processes and molecular events occurring in the system of interest. One area of major interest is the use of proteomics to identify diagnostic and prognostic biomarkers for different diseases as well as for various clinical phenotypes in organ transplantation that can advance targeted therapy for various forms of graft injury. Outcomes in organ transplantation can be potentially improved by identifying noninvasive biomarkers that will serve as triggers that predate graft injury, and can offer a means to customize patient treatment by differentiating among causes of acute and chronic graft injury. Proteomic and peptidomic strategies can be harnessed for frequent noninvasive measurements in tissue fluids, allowing for serial monitoring of organ disease. In this review, we describe the basic techniques used in proteomic and peptidomic approaches, point out special considerations in using these methods, and discuss their applications in recently published studies in organ transplantation.
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Affiliation(s)
- Tara K Sigdel
- Department of Pediatrics-Nephrology, Stanford University Medical School, Stanford University, Stanford, California 94305, USA
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Kohler M, Franz S, Regeniter A, Ikonen A, Walpurgis K, Thomas A, Schänzer W, Thevis M. Comparison of the urinary protein patterns of athletes by 2D-gel electrophoresis and mass spectrometryâa pilot study. Drug Test Anal 2009; 1:382-6. [DOI: 10.1002/dta.80] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Schlatzer DM, Dazard JE, Dharsee M, Ewing RM, Ilchenko S, Stewart I, Christ G, Chance MR. Urinary protein profiles in a rat model for diabetic complications. Mol Cell Proteomics 2009; 8:2145-58. [PMID: 19497846 DOI: 10.1074/mcp.m800558-mcp200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Diabetes mellitus is estimated to affect approximately 24 million people in the United States and more than 150 million people worldwide. There are numerous end organ complications of diabetes, the onset of which can be delayed by early diagnosis and treatment. Although assays for diabetes are well founded, tests for its complications lack sufficient specificity and sensitivity to adequately guide these treatment options. In our study, we employed a streptozotocin-induced rat model of diabetes to determine changes in urinary protein profiles that occur during the initial response to the attendant hyperglycemia (e.g. the first two months) with the goal of developing a reliable and reproducible method of analyzing multiple urine samples as well as providing clues to early markers of disease progression. After filtration and buffer exchange, urinary proteins were digested with a specific protease, and the relative amounts of several thousand peptides were compared across rat urine samples representing various times after administration of drug or sham control. Extensive data analysis, including imputation of missing values and normalization of all data was followed by ANOVA analysis to discover peptides that were significantly changing as a function of time, treatment and interaction of the two variables. The data demonstrated significant differences in protein abundance in urine before observable pathophysiological changes occur in this animal model and as function of the measured variables. These included decreases in relative abundance of major urinary protein precursor and increases in pro-alpha collagen, the expression of which is known to be regulated by circulating levels of insulin and/or glucose. Peptides from these proteins represent potential biomarkers, which can be used to stage urogenital complications from diabetes. The expression changes of a pro-alpha 1 collagen peptide was also confirmed via selected reaction monitoring.
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Affiliation(s)
- Daniela M Schlatzer
- Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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Miller WG, Bruns DE, Hortin GL, Sandberg S, Aakre KM, McQueen MJ, Itoh Y, Lieske JC, Seccombe DW, Jones G, Bunk DM, Curhan GC, Narva AS. Current issues in measurement and reporting of urinary albumin excretion. Clin Chem 2008; 55:24-38. [PMID: 19028824 DOI: 10.1373/clinchem.2008.106567] [Citation(s) in RCA: 234] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Urinary excretion of albumin indicates kidney damage and is recognized as a risk factor for progression of kidney disease and cardiovascular disease. The role of urinary albumin measurements has focused attention on the clinical need for accurate and clearly reported results. The National Kidney Disease Education Program and the IFCC convened a conference to assess the current state of preanalytical, analytical, and postanalytical issues affecting urine albumin measurements and to identify areas needing improvement. CONTENT The chemistry of albumin in urine is incompletely understood. Current guidelines recommend the use of the albumin/creatinine ratio (ACR) as a surrogate for the error-prone collection of timed urine samples. Although ACR results are affected by patient preparation and time of day of sample collection, neither is standardized. Considerable intermethod differences have been reported for both albumin and creatinine measurement, but trueness is unknown because there are no reference measurement procedures for albumin and no reference materials for either analyte in urine. The recommended reference intervals for the ACR do not take into account the large intergroup differences in creatinine excretion (e.g., related to differences in age, sex, and ethnicity) nor the continuous increase in risk related to albumin excretion. DISCUSSION Clinical needs have been identified for standardization of (a) urine collection methods, (b) urine albumin and creatinine measurements based on a complete reference system, (c) reporting of test results, and (d) reference intervals for the ACR.
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Affiliation(s)
- W Greg Miller
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA.
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Li SJ, Peng M, Li H, Liu BS, Wang C, Wu JR, Li YX, Zeng R. Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Res 2008; 37:D907-12. [PMID: 18978022 PMCID: PMC2686600 DOI: 10.1093/nar/gkn849] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recently, body fluids have widely become an important target for proteomic research and proteomic study has produced more and more body fluid related protein data. A database is needed to collect and analyze these proteome data. Thus, we developed this web-based body fluid proteome database Sys-BodyFluid. It contains eleven kinds of body fluid proteomes, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, human milk and amniotic fluid. Over 10,000 proteins are presented in the Sys-BodyFluid. Sys-BodyFluid provides the detailed protein annotations, including protein description, Gene Ontology, domain information, protein sequence and involved pathways. These proteome data can be retrieved by using protein name, protein accession number and sequence similarity. In addition, users can query between these different body fluids to get the different proteins identification information. Sys-BodyFluid database can facilitate the body fluid proteomics and disease proteomics research as a reference database. It is available at http://www.biosino.org/bodyfluid/.
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Affiliation(s)
- Su-Jun Li
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Pérès S, Molina L, Salvetat N, Granier C, Molina F. A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics. BMC Bioinformatics 2008; 9:460. [PMID: 18957120 PMCID: PMC2628390 DOI: 10.1186/1471-2105-9-460] [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: 06/04/2008] [Accepted: 10/28/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user. RESULTS We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects. CONCLUSION Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.
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Affiliation(s)
- Sabine Pérès
- Sysdiag CNRS FRE 3009 BIO-RAD, Cap delta/Parc Euromédecine, 1682 rue de la Valsière, CS 61003, 34184 Montpellier Cedex 4, France.
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35
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Coon JJ, Zürbig P, Dakna M, Dominiczak AF, Decramer S, Fliser D, Frommberger M, Golovko I, Good DM, Herget-Rosenthal S, Jankowski J, Julian BA, Kellmann M, Kolch W, Massy Z, Novak J, Rossing K, Schanstra JP, Schiffer E, Theodorescu D, Vanholder R, Weissinger EM, Mischak H, Schmitt-Kopplin P. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clin Appl 2008; 2:964. [PMID: 20130789 PMCID: PMC2815342 DOI: 10.1002/prca.200800024] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Indexed: 12/22/2022]
Abstract
Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. Capillary electrophoresis coupled to mass spectrometry (CE-MS), which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enabled the diagnosis, classification, and monitoring of a wide range of diseases. CE-MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level.
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Affiliation(s)
- Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Petra Zürbig
- Mosaiques diagnostics & therapeutics, Hannover, Germany
| | | | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Stéphane Decramer
- Department of Renal and Cardiac Remodelling, Inserm, U858/I2MR, Toulouse, France
- Université Toulouse III Paul Sabatier, Institut de Médecine Moléculaire de Rangueil, Toulouse, France
- Pediatric Nephrology Unit, Hopital des Enfants, CHU de Toulouse, Toulouse, France
| | - Danilo Fliser
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Moritz Frommberger
- Department of Ecological Chemistry, Helmholtz Center Munich German Research Center for Health and Environment, Neuherberg, Germany
| | - Igor Golovko
- Mosaiques diagnostics & therapeutics, Hannover, Germany
| | - David M. Good
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | - Walter Kolch
- The Beatson Institute for Cancer Research & Sir Henry Wellcome Functional Genomics Facility, University of Glasgow, Glasgow, UK
| | - Ziad Massy
- Departments of Clinical Pharmacology and Nephrology, INSERM, ERI-12, and Amiens University Hospital, UPJV, Amiens, France
| | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Joost P. Schanstra
- Department of Renal and Cardiac Remodelling, Inserm, U858/I2MR, Toulouse, France
- Université Toulouse III Paul Sabatier, Institut de Médecine Moléculaire de Rangueil, Toulouse, France
| | - Eric Schiffer
- Mosaiques diagnostics & therapeutics, Hannover, Germany
| | - Dan Theodorescu
- Department of Urology, University of Virginia, Charlottesville, VA, USA
| | - Raymond Vanholder
- Department of Internal Medicine, University Hospital Ghent, Ghent, Belgium
| | - Eva M. Weissinger
- Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Philippe Schmitt-Kopplin
- Department of Ecological Chemistry, Helmholtz Center Munich German Research Center for Health and Environment, Neuherberg, Germany
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Candiano G, Bruschi M, Petretto A, Santucci L, Del Boccio P, Urbani A, Bertoni E, Gusmano R, Salvadori M, Scolari F, Ghiggeri GM. Proteins and protein fragments in nephrotic syndrome: Clusters, specificity and mechanisms. Proteomics Clin Appl 2008; 2:956-63. [DOI: 10.1002/prca.200780157] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Indexed: 11/06/2022]
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37
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Hortin GL, Sviridov D. Analysis of molecular forms of albumin in urine. Proteomics Clin Appl 2008; 2:950-5. [DOI: 10.1002/prca.200780145] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Indexed: 11/10/2022]
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Mavroidis M, Panagopoulou P, Kostavasili I, Weisleder N, Capetanaki Y. A missense mutation in desmin tail domain linked to human dilated cardiomyopathy promotes cleavage of the head domain and abolishes its Z-disc localization. FASEB J 2008; 22:3318-27. [PMID: 18539904 DOI: 10.1096/fj.07-088724] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A missense mutation (Ile 451 to Met) at the tail domain of the muscle-specific intermediate filament protein desmin has been suggested to be a genetic cause of dilated cardiomyopathy. The Ile451Met mutation is located inside a conserved motif in the desmin tail domain, believed to have a potential role in the lateral packing of type III intermediate filaments. Nevertheless, the role of the type III intermediate filament tail domain remains elusive. To further study the role of this domain in the function of cardiomyocytes and in the development of cardiomyopathy, we generated transgenic mice expressing the mutant desmin(I451M) in the cardiac tissue. Analysis of hearts from transgenic animals revealed that mutant desmin loses its Z-disc localization but it can still associate with the intercalated discs, which, however, have an altered architecture, resembling other examples of dilated cardiomyopathy. This is the first report demonstrating a critical role of the desmin head and tail domains in the formation of the IF scaffold around Z discs. It is further suggested that in cardiomyocytes, an interplay between desmin tail and head domains is taking place, which potentially protects the amino terminus of desmin from specific proteases. The fact that the association with intercalated discs seems unchanged suggests that this association must take place through the desmin tail, in contrast to the head domain that is most possibly involved in the Z-disc binding.
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Affiliation(s)
- Manolis Mavroidis
- Cell Biology Division, Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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39
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Zerefos PG, Vlahou A. Urine sample preparation and protein profiling by two-dimensional electrophoresis and matrix-assisted laser desorption ionization time of flight mass spectroscopy. Methods Mol Biol 2008; 428:141-57. [PMID: 18287772 DOI: 10.1007/978-1-59745-117-8_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Urine represents the most easily attainable and consequently one of the most common samples in clinical analysis and diagnostics. However, urine is also considered one of the most difficult proteomic samples to work with due to its highly variable contents, as well as the presence of various proteins in low abundance or modified forms. In this chapter, we describe simple protocols and troubleshooting tips for urinary protein preparation and profiling by two-dimensional electrophoresis or directly via matrix-assisted laser desorption ionization time of flight mass spectroscopy. Direct dilution, protein precipitation, ultrafiltration, and solid phase extraction in combination to the above profiling technologies serve the means for reliable proteomics analysis of one of the most significant yet very complex biological samples.
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Affiliation(s)
- Panagiotis G Zerefos
- Division of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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40
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Roubelakis MG, Pappa KI, Bitsika V, Zagoura D, Vlahou A, Papadaki HA, Antsaklis A, Anagnou NP. Molecular and proteomic characterization of human mesenchymal stem cells derived from amniotic fluid: comparison to bone marrow mesenchymal stem cells. Stem Cells Dev 2008; 16:931-52. [PMID: 18047393 DOI: 10.1089/scd.2007.0036] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Human mesenchymal stem cells (hMSCs) constitute a population of multipotent adherent cells able to give rise to multiple mesenchymal lineages such as osteoblasts, adipocytes, or chondrocytes. So far, the most common source of MSCs has been the bone marrow (BM); however BM-MSC harvesting and processing exhibits major drawbacks and limitations. Thus, identification and characterization of alternative sources of MSCs are of great importance. In the present study, we isolated and expanded fetal MSCs from second-trimester amniotic fluid (AF). We documented that these cells are of embryonic origin, can differentiate under appropriate conditions into cell types derived from all three germ layers, and express the pluripotency marker Oct-4, the human Nanog protein, and the stage-specific embryonic antigen-4 (SSEA-4). Furthermore, we systematically tested the immunophenotype of cultured MSCs by flow cytometry analysis using a wide variety of markers. Direct comparison of this phenotype to the one derived from cultured BM-MSCs demonstrated that cultured MSCs from both sources exhibit similar expression patterns. Using the two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) approach, we have generated for the first time the protein map of cultured AF-MSCs by identifying 261 proteins, and we compared it directly to that of cultured BM-MSCs. The functional pattern of the identified proteins from both sources was similar. However, cultured AF-MSCs displayed a number of unique proteins related to proliferation and primitive phenotype, which may confer to the distinct features of the two types. Considering the easy access to this new cell source and the yield of expanded MSCs for stem cell research, AF may provide an excellent source of MSCs both for basic research and for potential therapeutic applications.
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Affiliation(s)
- Maria G Roubelakis
- Cell and Gene Therapy Laboratory, Centre of Basic Research II, Biomedical Research Foundation of the Academy of Athens (BRF), Athens, Greece
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Tran JC, Doucette AA. Gel-Eluted Liquid Fraction Entrapment Electrophoresis: An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation. Anal Chem 2008; 80:1568-73. [DOI: 10.1021/ac702197w] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- John C. Tran
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4J3
| | - Alan A. Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia, Canada B3H 4J3
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Abstract
The complementary fields of genomics and proteomics offer insights into the molecular mechanisms of diseases. While genomics seeks to define our genetic substrate, proteomics explores the structure and function of proteins, which are the end effectors of our genes. Proteomics has been revolutionized in the past decade by the application of techniques such as protein arrays, two-dimensional gel electrophoresis, and mass spectrometry. These techniques have tremendous potential for biomarker development, target validation, diagnosis, prognosis, and optimization of treatment in medical care, especially in the field of clinical oncology. We will discuss innovations in proteomic technologies and highlight their prospective applications to patient care.
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Affiliation(s)
- Amit S Dhamoon
- Medical Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr. MSC 1500, Bethesda, MD 20892, United States
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43
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Thongboonkerd V. Recent progress in urinary proteomics. Proteomics Clin Appl 2007; 1:780-91. [PMID: 21136734 DOI: 10.1002/prca.200700035] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Indexed: 11/08/2022]
Abstract
Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Molecular Biology Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. ,
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Kreunin P, Zhao J, Rosser C, Urquidi V, Lubman DM, Goodison S. Bladder cancer associated glycoprotein signatures revealed by urinary proteomic profiling. J Proteome Res 2007; 6:2631-9. [PMID: 17518487 PMCID: PMC2668245 DOI: 10.1021/pr0700807] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Current methods in the noninvasive detection and surveillance of bladder cancer via urine analysis include voided urine cytology (VUC) and some diagnostic urinary protein biomarkers; however, due to the poor sensitivity of VUC and high false-positive rates of currently available protein assays, detection of bladder cancer via urinalysis remains a challenge. In the study presented here, a rapid, high-sensitivity technique was developed to profile the N-linked glycoprotein component in naturally micturated human urine specimens. Concanavalin A (Con A) affinity chromatography coupled to nanoflow liquid chromatography was utilized to separate the complex peptide mixture prior to a linear ion trap MS analysis. Of 186 proteins identified with high confidence by multiple analyses, 40% were secreted proteins, 18% membrane proteins, and 14% extracellular proteins. In this study, the presence of several proteins appeared to be associated with the presence of bladder cancer, including alpha-1B-glycoprotein that was detected in all tumor-bearing patient samples but in none of the samples obtained from non-tumor-bearing individuals. The combination of Con A affinity chromatography and nano-LC/MS/MS provides an initial investigation of N-glycoproteins in complex biological samples and facilitates the identification of potential biomarkers of bladder cancer in noninvasively obtained human urine.
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Affiliation(s)
| | | | | | | | | | - Steve Goodison
- To whom correspondence should be addressed. Phone: (904) 244-6180. Fax: (904) 244-4667. E-mail:
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45
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Zerefos P, Prados J, Kossida S, Kalousis A, Vlahou A. Sample preparation and bioinformatics in MALDI profiling of urinary proteins. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 853:20-30. [PMID: 17537688 DOI: 10.1016/j.jchromb.2007.02.063] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 02/23/2007] [Indexed: 11/30/2022]
Abstract
One of the challenges of current proteomics research is identifying healthy and diseased mass spectrometric (MS) patterns within biological fluids. As a result, sample preparation methodologies, as well as the mathematical tools utilized for MS data analysis become pivotal. This study involves a thorough evaluation of the reproducibility and protein resolution that various urinary protein preparation methodologies provide in MALDI MS analysis. Several precipitation approaches, ultrafiltration, as well as direct dilution of urine in MALDI MS compatible buffers were applied in combination to a thorough bioinformatics analysis of the generated MS data. Our results indicate that ultrafiltration, as well as direct dilution of urine in TFA, can provide information rich and reproducible spectra for mass ranges up to 20 kDa. The importance of the presence of peak reproducibility filters when generating disease classification models is suggested.
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Affiliation(s)
- Panagiotis Zerefos
- Foundation for Biomedical Research of the Academy of Athens, Athens, Greece
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46
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Abstract
Urine represents a modified ultrafiltrate of plasma, with protein concentrations typically approximately 1000-fold lower than plasma. Urine’s low protein concentration might suggest it to be a less promising diagnostic specimen than plasma. However, urine can be obtained noninvasively and tests of many urinary proteins are well-established in clinical practice. Proteomic technologies expand opportunities to analyze urinary proteins, identifying more than 1000 proteins and peptides in urine. Urine offers a sampling of most plasma proteins, with increased proportions of low-molecular-weight protein and peptide components. Urine also offers enriched sampling of proteins released along the urinary tract. Although urine presents some challenges as a diagnostic specimen, its diverse range of potential markers offers great potential for diagnosis of both systemic and kidney diseases. Examples of clinical situations where this may be of value are for more sensitive detection of kidney transplant rejection or of renal toxicity of medications.
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Affiliation(s)
- Glen L Hortin
- National Institutes of Health, Department of Laboratory Medicine, Warren Magnuson Clinical Center, Building 10, Room 2C-407, Bethesda, MD 20892-1508, USA.
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47
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Fiedler GM, Baumann S, Leichtle A, Oltmann A, Kase J, Thiery J, Ceglarek U. Standardized peptidome profiling of human urine by magnetic bead separation and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin Chem 2007; 53:421-8. [PMID: 17272489 DOI: 10.1373/clinchem.2006.077834] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Peptidome profiling of human urine is a promising tool to identify novel disease-associated biomarkers; however, a wide range of preanalytical variables influence the results of peptidome analysis. Our aim was to develop a standardized protocol for reproducible urine peptidome profiling by means of magnetic bead (MB) separation followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). METHODS MBs with defined surface functionalities (hydrophobic interaction, cation exchange, and metal ion affinity) were used for peptide fractionation of urine. Mass accuracy and imprecision were calculated for 9 characteristic mass signals (M(r), 1000-10,000). Exogenous variables (instrument performance, urine sampling/storage conditions, freezing conditions, and freeze-thaw cycles) and endogenous variables (pH, urine salt and protein concentrations, and blood and bacteria interferences) were investigated with urine samples from 10 male and 10 female volunteers. RESULTS We detected 427 different mass signals in the urine of healthy donors. Within- and between-day imprecision in relative signal intensities ranged from 1% to 14% and from 4% to 16%, respectively. Weak cation-exchange and metal ion affinity MB preparations required adjustment of the urinary pH to 7. Storage time, storage temperature, the number of freeze-thaw cycles, and bacterial and blood contamination significantly influenced urine peptide patterns. Individual urine peptide patterns differed significantly within and between days. This imprecision was diminished by normalization to a urinary protein content of 3.5 microg. CONCLUSION This reliable pretreatment protocol allows standardization of preanalytical modalities and facilitates reproducible peptidome profiling of human urine by means of MB separation in combination with MALDI-TOF MS.
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Affiliation(s)
- Georg Martin Fiedler
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital, Leipzig, Germany
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