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Verscheure E, Stierum R, Schlünssen V, Lund Würtz AM, Vanneste D, Kogevinas M, Harding BN, Broberg K, Zienolddiny-Narui S, Erdem JS, Das MK, Makris KC, Konstantinou C, Andrianou X, Dekkers S, Morris L, Pronk A, Godderis L, Ghosh M. Characterization of the internal working-life exposome using minimally and non-invasive sampling methods - a narrative review. ENVIRONMENTAL RESEARCH 2023; 238:117001. [PMID: 37683788 DOI: 10.1016/j.envres.2023.117001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
During recent years, we are moving away from the 'one exposure, one disease'-approach in occupational settings and towards a more comprehensive approach, taking into account the totality of exposures during a life course by using an exposome approach. Taking an exposome approach however is accompanied by many challenges, one of which, for example, relates to the collection of biological samples. Methods used for sample collection in occupational exposome studies should ideally be minimally invasive, while at the same time sensitive, and enable meaningful repeated sampling in a large population and over a longer time period. This might be hampered in specific situations e.g., people working in remote areas, during pandemics or with flexible work hours. In these situations, using self-sampling techniques might offer a solution. Therefore, our aim was to identify existing self-sampling techniques and to evaluate the applicability of these techniques in an occupational exposome context by conducting a literature review. We here present an overview of current self-sampling methodologies used to characterize the internal exposome. In addition, the use of different biological matrices was evaluated and subdivided based on their level of invasiveness and applicability in an occupational exposome context. In conclusion, this review and the overview of self-sampling techniques presented herein can serve as a guide in the design of future (occupational) exposome studies while circumventing sample collection challenges associated with exposome studies.
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Affiliation(s)
- Eline Verscheure
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Stierum
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anne Mette Lund Würtz
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Dorian Vanneste
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Manolis Kogevinas
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Barbara N Harding
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Karin Broberg
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Mrinal K Das
- National Institute of Occupational Health, Oslo, Norway
| | - Konstantinos C Makris
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Corina Konstantinou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Xanthi Andrianou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Susan Dekkers
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | | | - Anjoeka Pronk
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium; Idewe, External Service for Prevention and Protection at work, Heverlee, Belgium.
| | - Manosij Ghosh
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium.
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Pajenda S, Wagner L, Gerges D, Herkner H, Tevdoradze T, Mechtler K, Schmidt A, Winnicki W. Urinary Collectrin (TMEM27) as Novel Marker for Acute Kidney Injury. Life (Basel) 2022; 12:life12091391. [PMID: 36143426 PMCID: PMC9503639 DOI: 10.3390/life12091391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 12/04/2022] Open
Abstract
Acute kidney injury (AKI) is a leading complication in hospitalized patients of different disciplines due to various aetiologies and is associated with the risk of chronic kidney disease, the need for dialysis and death. Since nephrons are not supplied with pain signals, kidney injury is mostly diagnosed by serum creatinine with a time delay. Recent work has shown that certain urinary biomarkers are available for early detection of AKI. In total, 155 subjects, including 102 patients with AKI at various stages and 53 subjects without AKI, were enrolled, and their course and laboratory data were recorded. Urinary collectrin (TMEM27) was measured by a commercially available ELISA assay. Changes in serum creatinine were used to determine AKI stage. Patients with AKI presented with significantly lower levels of urinary collectrin compared to patients without AKI (1597 ± 1827 pg/mL vs. 2855 ± 2073; p = 0.001). Collectrin was found to inversely correlate with serum creatinine and stages of AKI. Collectrin levels were lowest in AKI stage III (1576 ± 1686 pg/mL; p = 0.001) and also significantly lower in stage II (1616 ± 2148 pg/mL; p = 0.021) and stage I (1630 ± 1956 pg/mL; p = 0.019) compared to subjects without AKI. An optimal minimum collectrin cut-off value of 1606 [95% CI 1258 to 1954] pg/mL was determined to detect AKI. In conclusion, urinary collectrin represents an indicator of AKI that, unlike all other established AKI biomarkers, decreases with stage of AKI and thus may be associated with a novel pathogenic pathway.
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Affiliation(s)
- Sahra Pajenda
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, 1090 Vienna, Austria
| | - Ludwig Wagner
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence:
| | - Daniela Gerges
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, 1090 Vienna, Austria
| | - Harald Herkner
- Department of Emergency Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Tamar Tevdoradze
- Department of Renal Replacement Therapy, Nephrology and Transplantation, Tbilisi State Medical University and Ingorokva High Medical Technology University Clinic, Tbilisi 0144, Georgia
| | - Karl Mechtler
- ProtChem Facility, IMP-IMBA, Research Institute of Molecular Pathology, 1030 Vienna, Austria
| | - Alice Schmidt
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, 1090 Vienna, Austria
| | - Wolfgang Winnicki
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, 1090 Vienna, Austria
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3
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A comparative proteomic analysis to define the influencing factors on gingival crevicular fluid using LC-MS/MS. J Proteomics 2022; 252:104421. [PMID: 34801745 DOI: 10.1016/j.jprot.2021.104421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 12/18/2022]
Abstract
Gingival crevicular fluid (GCF) is a promising biofluid for disease identification and biomarker searching in periodontology. This study aimed to investigate the possible influencing factors, including tooth site, sex and age, on the normal GCF proteome. Forty periodontal healthy adults were randomly divided into a training group and a testing group. In the training group, GCF samples from 12 adults were analyzed using the iTRAQ 2D LC-MS/MS method. The influencing factors, tooth site (including periodontitis-susceptible and -insusceptible tooth sites), sex and age, and related differential proteins were defined and functionally annotated. The important differential proteins from 28 adults in the testing group were then validated by PRM analysis. An average of approximately 5 differential proteins were found between tooth sites of periodontitis-susceptible and -insusceptible sites. Eighty-five differentially expressed proteins were obtained between sexes in the young group, while only 7 sex-associated proteins were found in the old group. A total of 203 and 235 age-associated proteins were found in the male and female groups, respectively. The differential protein functional annotation showed that sex-related proteins were mainly related to immune function and metabolism, and age-related proteins were primarily associated with inflammation, lipid metabolism and immune function. In the testing group, a total of 4 sex-related proteins and 12 age-related proteins were validated by PRM analysis. SIGNIFICANCE: The influences of tooth site, sex and age in GCF proteomics in periodontal health were firstly analyzed using LC-MS/MS. Tooth site showed a small influence on the GCF proteome. The sex effect was significant in young adults, but its influence in old adults is small. Age is an important impact factor for the GCF proteome. These findings enrich the knowledge about the normal GCF proteome and might benefit future disease analyses.
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Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J. HBFP: a new repository for human body fluid proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6395039. [PMID: 34642750 PMCID: PMC8516408 DOI: 10.1093/database/baab065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Body fluid proteome has been intensively studied as a primary source for disease
biomarker discovery. Using advanced proteomics technologies, early research
success has resulted in increasingly accumulated proteins detected in different
body fluids, among which many are promising biomarkers. However, despite a
handful of small-scale and specific data resources, current research is clearly
lacking effort compiling published body fluid proteins into a centralized and
sustainable repository that can provide users with systematic analytic tools. In
this study, we developed a new database of human body fluid proteome (HBFP) that
focuses on experimentally validated proteome in 17 types of human body fluids.
The current database archives 11 827 unique proteins reported by 164
scientific publications, with a maximal false discovery rate of 0.01 on both the
peptide and protein levels since 2001, and enables users to query, analyze and
download protein entries with respect to each body fluid. Three unique features
of this new system include the following: (i) the protein annotation page
includes detailed abundance information based on relative qualitative measures
of peptides reported in the original references, (ii) a new score is calculated
on each reported protein to indicate the discovery confidence and (iii) HBFP
catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of
nine amino acids according to the Human Proteome Project Data Interpretation
Guidelines, while the remaining 4473 proteins have more than two unique peptides
without given sequence information. As an important resource for human protein
secretome, we anticipate that this new HBFP database can be a powerful tool that
facilitates research in clinical proteomics and biomarker discovery. Database URL:https://bmbl.bmi.osumc.edu/HBFP/
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Affiliation(s)
- Dan Shao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA.,Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China.,Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xueteng Cui
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yufei Li
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yao Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 310G Lincoln tower, 1800 cannon drive, Columbus, OH 43210, USA
| | - Wei Du
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA
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António M, Vitorino R, Daniel-da-Silva AL. Gold nanoparticles-based assays for biodetection in urine. Talanta 2021; 230:122345. [PMID: 33934794 DOI: 10.1016/j.talanta.2021.122345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Urine is a biofluid easy to collect through a non-invasive technique that allows collecting a large volume of sample. The use of urine for disease diagnosis is not yet well explored. However, it has gained attention over the last three years. It has been applied in the diagnosis of several illnesses such as kidney disease, bladder cancer, prostate cancer and cardiovascular diseases. In the last decade, gold nanoparticles (Au NPs) have attracted attention in biosensors' development for the diagnosis of diseases due to their electrical and optical properties, ability to conjugate with biomolecules, high sensitivity, and selectivity. Therefore, this article aims to present a comprehensive view of state of the art on the advances made in the quantification of analytes in urinary samples using AuNPs based assays, with a focus on protein analysis. The type of diagnosis methods, the Au NPs synthesis approaches and the strategies for surface modification aiming at selectivity towards the different targets are highlighted.
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Affiliation(s)
- Maria António
- CICECO-Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Rui Vitorino
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, 3810-193, Portugal; Department of Surgery and Physiology, Cardiovascular R&D Center, Faculty of Medicine of the University of Porto, Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal; LAQV-REQUIMTE, Chemistry Department, University of Aveiro, Aveiro, Portugal.
| | - Ana L Daniel-da-Silva
- CICECO-Aveiro Institute of Materials, Chemistry Department, University of Aveiro, 3810-193, Aveiro, Portugal.
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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: 27] [Impact Index Per Article: 9.0] [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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Watanabe Y, Hirao Y, Kasuga K, Tokutake T, Kitamura K, Niida S, Ikeuchi T, Nakamura K, Yamamoto T. Urinary Apolipoprotein C3 Is a Potential Biomarker for Alzheimer's Disease. Dement Geriatr Cogn Dis Extra 2020; 10:94-104. [PMID: 33082773 PMCID: PMC7548924 DOI: 10.1159/000509561] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Biomarkers of Alzheimer's disease (AD) that can easily be measured in routine health checkups are desirable. Urine is a source of biomarkers that can be collected easily and noninvasively. We previously reported on the comprehensive profile of the urinary proteome of AD patients and identified proteins estimated to be significantly increased or decreased in AD patients by a label-free quantification method. The present study aimed to validate urinary levels of proteins that significantly differed between AD and control samples from our proteomics study (i.e., apolipoprotein C3 [ApoC3], insulin-like growth factor-binding protein 3 [Igfbp3], and apolipoprotein D [ApoD]). METHODS Enzyme-linked immunosorbent assays (ELISAs) were performed using urine samples from the same patient and control groups analyzed in the previous proteomics study (18 AD and 18 controls, set 1) and urine samples from an independent group of AD patients and controls (13 AD, 5 mild cognitive impairment [MCI], and 32 controls) from the National Center for Geriatrics and Gerontology Biobank (set 2). RESULTS In set 1, the crude urinary levels of ApoD, Igfbp3, and creatinine-adjusted ApoD were significantly higher in the AD group relative to the control group (p = 0.003, p = 0.002, and p = 0.019, respectively), consistent with our previous proteomics results. In set 2, however, the crude urinary levels of Igfbp3 were significantly lower in the AD+MCI group than in the control group (p = 0.028), and the levels of ApoD and ApoC3 did not differ significantly compared to the control group. Combined analysis of all samples revealed creatinine-adjusted ApoC3 levels to be significantly higher in the AD+MCI group (p = 0.015) and the AD-only group (p = 0.011) relative to the control group. CONCLUSION ApoC3 may be a potential biomarker for AD, as validated by ELISA. Further analysis of ApoC3 as a urinary biomarker for AD is warranted.
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Affiliation(s)
- Yumi Watanabe
- aDivision of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yoshitoshi Hirao
- bBiofluid Biomarker Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kensaku Kasuga
- cDepartment of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Takayoshi Tokutake
- dDepartment of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kaori Kitamura
- aDivision of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shumpei Niida
- eResearch Institute, National Center for Geriatrics and Gerontology, Obu, Japan
| | - Takeshi Ikeuchi
- cDepartment of Molecular Genetics, Brain Research Institute, Niigata University, Niigata, Japan
| | - Kazutoshi Nakamura
- aDivision of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tadashi Yamamoto
- bBiofluid Biomarker Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- fDepartment of Clinical Laboratory, Shinrakuen Hospital, Niigata, Japan
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Reiter T, Knafl D, Agis H, Mechtler K, Wagner L, Winnicki W. Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders. PeerJ 2019; 7:e7819. [PMID: 31592189 PMCID: PMC6778432 DOI: 10.7717/peerj.7819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/03/2019] [Indexed: 11/20/2022] Open
Abstract
Background Monoclonal overproduction of kappa and/or lambda light chains might result in renal light chain deposition disease. Light chain associated cast nephropathy and renal AL-amyloidosis represent two further pathologies going along with monoclonal gammopathy of renal significance and multiple myeloma. While cast nephropathy often manifests with acute kidney injury, AL-amyloidosis is rather accompanied with chronic kidney disease. Methods Urine samples were collected from 17 patients with multiple myeloma or monoclonal gammopathy. The urine sediment was stained for cast morphology by H/E and light chain immunofluorescence. Following micro-selection of casts under microscope, proteomic analysis of casts was performed by mass spectrometry. Sucrose gradient sedimentation was employed and light chain architecture examined by immunoblotting. Uromodulin was measured by ELISA in sucrose gradient fractions. Results Urinary casts were observed of about 30 µm in diameter by H/E staining and under immunofluorescence microscopy. Casts with a diameter of 20 µm were observed as a novel variant. Proteome analysis showed that in addition to the expected light chain variants produced by the malignant clone of plasma cells, also histones such as H2B and cathepsin B were contained. Uromodulin was not detectable in urinary casts of all patients. All eleven patients with lambda light chains showed predominant dimerized light chains in the urine immunoblot. Six patients with kappa light chains presented with predominantly monomeric forms of light chains in the immunoblot. The densitometric evaluated ratio of lambda dimers vs. monomers was significantly higher (2.12 ± 0.75) when compared with the ratio of kappa dimers vs. monomers (0.64 ± 0.47), p = 0.00001. Aggregates of light chains separated in part into denser sucrose fractions. Conclusion This work on urinary casts and light chains demonstrates that hyaline tubular casts represent a complex formation of protein-protein aggregates with histones and cathepsin B identified as novel cast components. Apart from the proteomic composition of the casts, also the formation of the light chains and aggregates is of relevance. Dimerized light chains, which are typical for lambda paraproteins, might be less dialyzable than monomeric forms and may therefore identify patients less responsive to high cut-off dialysis.
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Affiliation(s)
- Thomas Reiter
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Daniela Knafl
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Hermine Agis
- Department of Medicine I, Division of Oncology, Medical University of Vienna, Vienna, Austria
| | - Karl Mechtler
- ProtChem Facility, IMP-IMBA, Research Institute of Molecular Pathology, Vienna, Austria
| | - Ludwig Wagner
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
| | - Wolfgang Winnicki
- Department of Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Vienna, Austria
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Shao C, Zhao M, Chen X, Sun H, Yang Y, Xiao X, Guo Z, Liu X, Lv Y, Chen X, Sun W, Wu D, Gao Y. Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences. Mol Cell Proteomics 2019; 18:1110-1122. [PMID: 30894400 PMCID: PMC6553935 DOI: 10.1074/mcp.ra119.001343] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/15/2019] [Indexed: 12/15/2022] Open
Abstract
Disease biomarkers are the measurable changes associated with a pathophysiological process. Without homeostatic control, urine accumulates systematic changes in the body. Thus, urine is an attractive biological material for the discovery of disease biomarkers. One of the major bottlenecks in urinary biomarker discovery is that the concentration and composition of urinary proteins are influenced by many physiological factors. To elucidate the individual variation and related factors influencing the urinary proteome, we comprehensively analyzed the urine samples from healthy adult donors (aged 20-69 years). Co-expression network analysis revealed protein clusters representing the metabolic status, gender-related differences and age-related differences in urinary proteins. In particular, we demonstrated that gender is a crucial factor contributing to individual variation. Proteins that were increased in the male urine samples include prostate-secreted proteins and TIMP1, a protein whose abundance alters under various cancers and renal diseases; however, the proteins that were increased in the female urine samples have known functions in the immune system. Nine gender-related proteins were validated on 85 independent samples by multiple reaction monitoring. Five of these proteins were further used to build a model that could accurately distinguish male and female urine samples with an area under curve value of 0.94. Based on the above results, we strongly suggest that future biomarker investigations should consider gender as a crucial factor in experimental design and data analysis. Finally, reference intervals of each urinary protein were estimated, providing a baseline for the discovery of abnormalities.
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Affiliation(s)
- Chen Shao
- From the ‡Center for Bioinformatics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
- §State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences(Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Mindi Zhao
- ¶Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Beijing, 100730, China
- ‖Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xizhao Chen
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Haidan Sun
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Yehong Yang
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xiaoping Xiao
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
- §§Cytology Lab, Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Science, Peking Union Medical College, Beijing, China
| | - Zhengguang Guo
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Xiaoyan Liu
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College
| | - Yang Lv
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Xiangmei Chen
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Wei Sun
- ‡‡Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College;
| | - Di Wu
- **Department of Nephrology, Chinese PLA General Hospital, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China;
| | - Youhe Gao
- ¶¶Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing, China
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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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11
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A comprehensive profile and inter-individual variations analysis of the human normal amniotic fluid proteome. J Proteomics 2018; 192:1-9. [PMID: 29684686 DOI: 10.1016/j.jprot.2018.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/23/2018] [Accepted: 04/14/2018] [Indexed: 11/21/2022]
Abstract
Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 14 high-abundance proteins. Each individual AF sample was used to analyze inter-individual variations with iTRAQ method. As a result, a total of 2881 non-redundant proteins were identified, and 1624 proteins were quantified based on the peak intensity-based semi-quantification (iBAQ) method. Gene Ontology (GO) analysis showed that the AF proteome was enriched in extracellular region and extracellular matrix. Further function annotation showed that the top canonical pathway was axonal guidance signaling. The inter-individual variation analysis of 7 individual AF samples showed that the median inter-individual CV (Coefficient of variation) was 0.22. iBAQ quantification analysis revealed that the inter-individual variations were not correlated with protein abundance. GO analysis indicated that intracellular proteins tended to have higher CVs, and extracellular proteins tended to have lower CVs. These data will contribute to a better understanding of amniotic fluid proteomic analysis and biomarker discovery. SIGNIFICANCE: Amniotic fluid is an important potential source of biomarkers for identifying fetal pathologies. This study provided a large database for the normal human amniotic fluid proteome and analysis of inter-individual variations in amniotic fluid proteomes, which will offer a baseline reference for further AF proteomic analysis and pregnancy-related disease biomarker discovery.
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12
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Ho ME, Quek SI, True LD, Seiler R, Fleischmann A, Bagryanova L, Kim SR, Chia D, Goodglick L, Shimizu Y, Rosser CJ, Gao Y, Liu AY. Bladder cancer cells secrete while normal bladder cells express but do not secrete AGR2. Oncotarget 2017; 7:15747-56. [PMID: 26894971 PMCID: PMC4941274 DOI: 10.18632/oncotarget.7400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/05/2016] [Indexed: 11/30/2022] Open
Abstract
Anterior gradient 2 (AGR2) is a cancer-associated secreted protein found predominantly in adenocarcinomas. Given its ubiquity in solid tumors, cancer-secreted AGR2 could be a useful biomarker in urine or blood for early detection. However, normal organs express and might also secrete AGR2, which would impact its utility as a cancer biomarker. Uniform AGR2 expression is found in the normal bladder urothelium. Little AGR2 is secreted by the urothelial cells as no measurable amounts could be detected in urine. The urinary proteomes of healthy people contain no listing for AGR2. Likewise, the blood proteomes of healthy people also contain no significant peptide counts for AGR2 suggesting little urothelial secretion into capillaries of the lamina propria. Expression of AGR2 is lost in urothelial carcinoma, with only 25% of primary tumors observed to retain AGR2 expression in a cohort of lymph node-positive cases. AGR2 is secreted by the urothelial carcinoma cells as urinary AGR2 was measured in the voided urine of 25% of the cases analyzed in a cohort of cancer vs. non-cancer patients. The fraction of AGR2-positive urine samples was consistent with the fraction of urothelial carcinoma that stained positive for AGR2. Since cancer cells secrete AGR2 while normal cells do not, its measurement in body fluids could be used to indicate tumor presence. Furthermore, AGR2 has also been found on the cell surface of cancer cells. Taken together, secretion and cell surface localization of AGR2 are characteristic of cancer, while expression of AGR2 by itself is not.
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Affiliation(s)
- Melissa E Ho
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.,Present address: University of California San Francisco Medical Center, San Francisco, CA, USA
| | - Sue-Ing Quek
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.,Present address: Singapore Polytechnic, Center for Biomedical & Life Sciences, Singapore
| | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Roland Seiler
- Department of Urology, University Hospital of Bern, Bern, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, University Hospital of Bern, Bern, Switzerland
| | - Lora Bagryanova
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sara R Kim
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Lee Goodglick
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | | | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alvin Y Liu
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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13
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Thölking G, Schuette-Nuetgen K, Vogl T, Dobrindt U, Kahl BC, Brand M, Pavenstädt H, Suwelack B, Koch R, Reuter S. Male kidney allograft recipients at risk for urinary tract infection? PLoS One 2017; 12:e0188262. [PMID: 29145515 PMCID: PMC5690643 DOI: 10.1371/journal.pone.0188262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/05/2017] [Indexed: 12/31/2022] Open
Abstract
Background Urinary tract infection (UTI) is the most common infection after renal transplantation (RTx). Although female sex is a well-known risk factor for the development of UTI after RTx, the role of the donor sex in this context remains unclear. Methods In this case control study 6,763 RTx cases were screened for UTI when presenting at our transplant outpatient clinics. 102 different RTx patients fulfilled the inclusion criteria and were compared to 102 controls. Data on renal function was prospectively followed for 12 months. Results were compared to a previous RTx cohort from our transplant center. Additionally, we assessed the immunological response of leukocytes from 58 kidney recipients and 16 controls to lipopolysaccharide stimulation. Result After identification by univariate analysis, multivariate logistic regression analysis indicated female sex, minor height, advanced age and male kidney allograft sex to be associated with the occurrence of UTI after RTx. Female recipients who received male grafts had the best renal function 12 months after presentation. However, leukocyte response of recipients to lipopolysaccharide was impaired irrespective of donor and recipient sex to the same extend. Conclusions We conclude from our data that male kidney allografts are associated with the occurrence of UTI after RTx but did not influence the response of leukocytes to lipopolysaccharide. Further prospective studies are needed to identify the underlying mechanisms of higher male kidney donor dependent UTI.
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Affiliation(s)
- Gerold Thölking
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, Münster, Germany
- * E-mail:
| | - Katharina Schuette-Nuetgen
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, Münster, Germany
| | - Thomas Vogl
- Institute of Immunology, University of Münster, Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Barbara C. Kahl
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Marcus Brand
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, Münster, Germany
| | - Hermann Pavenstädt
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, Münster, Germany
| | - Barbara Suwelack
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, Münster, Germany
| | - Raphael Koch
- Institute of Biostatistics and Clinical Research, University of Münster, Münster, Germany
| | - Stefan Reuter
- Department of Medicine D, Division of General Internal Medicine, Nephrology and Rheumatology, University Hospital Münster, Münster, Germany
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14
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Gianazza E, Miller I, Guerrini U, Palazzolo L, Parravicini C, Eberini I. Gender proteomics I. Which proteins in non-sexual organs. J Proteomics 2017; 178:7-17. [PMID: 28988882 DOI: 10.1016/j.jprot.2017.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Differences related to gender have long been neglected but recent investigations show that they are widespread and may be recognized with all types of omics approaches, both in tissues and in biological fluids. Our review compiles evidence collected with proteomics techniques in our species, mainly focusing on baseline parameters in non-sexual organs in healthy men and women. Data from human specimens had to be replaced with information from other mammals every time invasive procedures of sample procurement were involved. SIGNIFICANCE As our knowledge, and the methods to build it, get refined, gender differences need to receive more and more attention, as they influence the outcome of all aspects in lifestyle, including diet, exercise and environmental factors. In turn this background modulates a differential susceptibility to some disease, or a different pathogenetic mechanism, depending on gender, and a different response to pharmacological therapy. Preparing this review we meant to raise awareness about the gender issue. We anticipate that more and more often, in the future, separate evaluations will be carried out on male and female subjects as an alternative - and an upgrade - to the current approach of reference and test groups being 'matched for age and sex'.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy.
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Wien, Austria
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti 9, I-20133 Milano, Italy
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15
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Bekiares N, Krueger CG, Meudt JJ, Shanmuganayagam D, Reed JD. Effect of Sweetened Dried Cranberry Consumption on Urinary Proteome and Fecal Microbiome in Healthy Human Subjects. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 22:145-153. [PMID: 28618237 PMCID: PMC5810433 DOI: 10.1089/omi.2016.0167] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The relationship among diet, human health, and disease is an area of growing interest in biomarker research. Previous studies suggest that the consumption of cranberries (Vaccinium macrocarpon) could beneficially influence urinary and digestive health. The present study sought to determine if daily consumption of sweetened dried cranberries (SDC) changes the urinary proteome and fecal microbiome, as determined in a prospective sample of 10 healthy individuals. Baseline urine and fecal samples were collected from the subjects in the fasted (8-12 h) state. The subjects then consumed one serving (42 g) of SDC daily with lunch for 2 weeks. Urine and fecal samples were collected again the day after 2 weeks of SDC consumption. Orbitrap Q-Exactive mass spectrometry of urinary proteins showed that consumption of SDC resulted in changes to 22 urinary proteins. Multiplex sequencing of 16S ribosomal RNA genes in fecal samples indicated changes in relative abundance of several bacterial taxonomic units after consumption of SDC. There was a shift in the Firmicutes:Bacteroidetes ratio, increases in commensal bacteria, and decreases or the absence of bacteria associated with negative health effects. A decrease in uromodulin in all subjects and an increase in Akkermansia bacteria in most subjects were observed and warrant further investigation. Future larger clinical studies with multiomics and multitissue sampling designs are required to determine the effects of SDC consumption on nutrition and health.
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Affiliation(s)
- Nell Bekiares
- 1 Department of Animal Sciences, Reed Research Group, University of Wisconsin-Madison , Madison, Wisconsin
| | - Christian G Krueger
- 1 Department of Animal Sciences, Reed Research Group, University of Wisconsin-Madison , Madison, Wisconsin
| | - Jennifer J Meudt
- 2 Department of Animal Sciences, Biomedical and Genomic Research Group, University of Wisconsin-Madison , Madison, Wisconsin
| | - Dhanansayan Shanmuganayagam
- 2 Department of Animal Sciences, Biomedical and Genomic Research Group, University of Wisconsin-Madison , Madison, Wisconsin
| | - Jess D Reed
- 1 Department of Animal Sciences, Reed Research Group, University of Wisconsin-Madison , Madison, Wisconsin
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16
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Pajenda S, Mechtler K, Wagner L. Urinary neprilysin in the critically ill patient. BMC Nephrol 2017; 18:172. [PMID: 28545475 PMCID: PMC5445475 DOI: 10.1186/s12882-017-0587-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 05/16/2017] [Indexed: 02/06/2023] Open
Abstract
Background Critically ill patients in intensive care face hazardous conditions. Among these, acute kidney injury (AKI) is frequently seen as a result of sepsis. Early diagnosis of kidney injury is of the utmost importance in the guidance of interventions or avoidance of treatment-induced kidney injury. On these grounds, we searched for markers that could indicate proximal tubular cell injury. Methods Urine samples of 90 patients admitted to the intensive or intermediate care unit were collected over 2 to 5 days. The biomarker neprilysin (NEP) was investigated in urine using several methods such as dot blot, ELISA and immunofluorescence of urinary casts. Fifty-five healthy donors acted as controls. Results NEP was highly significantly elevated in the urine of patients who suffered AKI according to the KDIGO criteria in comparison to healthy controls. It was also found to be elevated in ICU patients without overt signs of AKI according to serum creatinine changes, however they were suffering from potential nephrotoxic insults. According to our findings, urinary NEP is indicative of epithelial cell alterations at the proximal tubule. This was elaborated in ICU patients when ghost fragments and NEP+ microvesicles were observed in urinary sediment cytopreparations. Furthermore, NEP+ immunofluorescence of healthy kidney tissue showed staining at the proximal tubules. Conclusions NEP, a potential marker for proximal tubular epithelia, can be measured in urine. This does not originate from leakage of elevated serum levels, but indicates proximal tubular cell alterations such as brush border severing, which can heal in most cases.
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Affiliation(s)
- Sahra Pajenda
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria.
| | - Karl Mechtler
- ProtChem Facility, IMP-IMBA - Research Institute of Molecular Pathology, Dr. Bohr Gasse 3, 1030, Vienna, Austria
| | - Ludwig Wagner
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
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17
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Cai M, Li W, Gao JJ, Wang Z, Zhou ZX, Han Y, Sun YL, Zhao XH. Significance of detection of urinary cathepsin D in patients with colorectal cancer liver metastasis. Shijie Huaren Xiaohua Zazhi 2016; 24:2170-2177. [DOI: 10.11569/wcjd.v24.i14.2170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM: To find a more economical method for monitoring colorectal carcinoma liver metastasis by detecting whether cathepsin D can be used as a urinary biomarker of colorectal carcinoma liver metastasis.
METHODS: Random mid-stream urine samples were collected from patients with colorectal carcinoma with or without liver metastasis. The urine protein was enriched on NC membrane through pumping filtration, and Western blot was used to detect the concentration of cathepsin D after elution. Urine creatine was used to normalise the result.
RESULTS: The enriched protein showed a good quality and Western blot results indicated that the concentration of cathepsin D in urine of patients with colorectal carcinoma liver metastasis was significantly higher than those of healthy controls and CRC patients without metastasis.
CONCLUSION: The method of urine protein enrichment allows to obtain high quality urine protein quickly, and urinary cathepsin D may serve as a potential biomarker of colorectal carcinoma liver metastasis.
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18
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Wu J, Gao Y. Physiological conditions can be reflected in human urine proteome and metabolome. Expert Rev Proteomics 2015; 12:623-36. [PMID: 26472227 DOI: 10.1586/14789450.2015.1094380] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biomarkers are the measurable changes associated with physiological or pathophysiological processes. Urine, unlike blood, lacks mechanisms for maintaining homeostasis: it is therefore an ideal source of biomarkers that can reflect systemic changes. Urinary proteome and metabolome have been studied for their diagnostic capabilities, ability to monitor disease and prognostic utility. In this review, the effects of common physiological conditions such as gender, age, diet, daily rhythms, exercise, hormone status, lifestyle and extreme environments on human urine are discussed. These effects should be considered when biomarker studies of diseases are conducted. More importantly, if physiological changes can be reflected in urine, we have reason to expect that urine will become widely used to detect small and early changes in pathological and/or pharmacological conditions.
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Affiliation(s)
- Jianqiang Wu
- a 1 Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Youhe Gao
- a 1 Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.,b 2 Department of Biochemistry and Molecular Biology, Beijing Normal University, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing, 100875, China
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19
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Gruppen EG, Riphagen IJ, Connelly MA, Otvos JD, Bakker SJL, Dullaart RPF. GlycA, a Pro-Inflammatory Glycoprotein Biomarker, and Incident Cardiovascular Disease: Relationship with C-Reactive Protein and Renal Function. PLoS One 2015; 10:e0139057. [PMID: 26398105 PMCID: PMC4580603 DOI: 10.1371/journal.pone.0139057] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/07/2015] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE GlycA is a novel nuclear magnetic resonance spectroscopy-measured biomarker of systemic inflammation. We determined whether GlycA is associated with incident cardiovascular disease (CVD) in men and women, examined whether this association with CVD is modified by renal function, and compared this association with high sensitivity C-reactive protein (hsCRP). RESEARCH DESIGN AND METHODS A prospective cohort study was performed among 4,759 subjects (PREVEND study) without a history of CVD and cancer. Incident CVD was defined as the combined endpoint of cardiovascular morbidity and mortality. Cox regression analyses were used to examine associations of baseline GlycA and hsCRP with CVD. RESULTS 298 first CVD events occurred during a median follow-up of 8.5 years. After adjustment for clinical and lipid measures the hazard ratio (HR) for CVD risk in the highest GlycA quartile was 1.58 (95% CI, 1.05-2.37, P for trend = 0.004). This association was similar after further adjustment for renal function (estimated glomerular filtration rate and urinary albumin excretion). After additional adjustment for hsCRP, GlycA was still associated with incident CVD (HR: 1.16 per SD change (95% CI, 1.01-1.33), P = 0.04). Similar results were obtained for hsCRP (HR per SD change after adjustment for GlycA: 1.17 (95% CI 1.17 (95% CI, 1.01-3.60), P = 0.04). CVD risk was highest in subjects with simultaneously higher GlycA and hsCRP (fully adjusted HR: 1.79 (95% CI, 1.31-2.46), P<0.001). CONCLUSION GlycA is associated with CVD risk in men and women, independent of renal function. The association of GlycA with incident CVD is as strong as that of hsCRP.
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Affiliation(s)
- Eke G Gruppen
- Department of Nephrology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands; Department of Endocrinology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ineke J Riphagen
- Department of Nephrology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | | | - James D Otvos
- LabCorp, Raleigh, North Carolina, United States of America
| | - Stephan J L Bakker
- Department of Nephrology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Robin P F Dullaart
- Department of Endocrinology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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20
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Radon TP, Massat NJ, Jones R, Alrawashdeh W, Dumartin L, Ennis D, Duffy SW, Kocher HM, Pereira SP, Guarner posthumous L, Murta-Nascimento C, Real FX, Malats N, Neoptolemos J, Costello E, Greenhalf W, Lemoine NR, Crnogorac-Jurcevic T. Identification of a Three-Biomarker Panel in Urine for Early Detection of Pancreatic Adenocarcinoma. Clin Cancer Res 2015; 21:3512-21. [PMID: 26240291 PMCID: PMC4539580 DOI: 10.1158/1078-0432.ccr-14-2467] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE Noninvasive biomarkers for early detection of pancreatic ductal adenocarcinoma (PDAC) are currently not available. Here, we aimed to identify a set of urine proteins able to distinguish patients with early-stage PDAC from healthy individuals. EXPERIMENTAL DESIGN Proteomes of 18 urine samples from healthy controls, chronic pancreatitis, and patients with PDAC (six/group) were assayed using GeLC/MS/MS analysis. The selected biomarkers were subsequently validated with ELISA assays using multiple logistic regression applied to a training dataset in a multicenter cohort comprising 488 urine samples. RESULTS LYVE-1, REG1A, and TFF1 were selected as candidate biomarkers. When comparing PDAC (n = 192) with healthy (n = 87) urine specimens, the resulting areas under the receiver-operating characteristic curves (AUC) of the panel were 0.89 [95% confidence interval (CI), 0.84-0.94] in the training (70% of the data) and 0.92 (95% CI, 0.86-0.98) in the validation (30% of the data) datasets. When comparing PDAC stage I-II (n = 71) with healthy urine specimens, the panel achieved AUCs of 0.90 (95% CI, 0.84-0.96) and 0.93 (95% CI, 0.84-1.00) in the training and validation datasets, respectively. In PDAC stage I-II and healthy samples with matching plasma CA19.9, the panel achieved a higher AUC of 0.97 (95% CI, 0.94-0.99) than CA19.9 (AUC = 0.88; 95% CI, 0.81-0.95, P = 0.005). Adding plasma CA19.9 to the panel increased the AUC from 0.97 (95% CI, 0.94-0.99) to 0.99 (95% CI, 0.97-1.00, P = 0.04), but did not improve the comparison of stage I-IIA PDAC (n = 17) with healthy urine. CONCLUSIONS We have established a novel, three-protein biomarker panel that is able to detect patients with early-stage pancreatic cancer in urine specimens.
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Affiliation(s)
- Tomasz P Radon
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nathalie J Massat
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
| | | | - Wasfi Alrawashdeh
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Laurent Dumartin
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Darren Ennis
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Stephen W Duffy
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, London, United Kingdom
| | - Hemant M Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Stephen P Pereira
- Institute for Liver and Digestive Health, University College London, London, United Kingdom
| | | | | | - Francisco X Real
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Núria Malats
- Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - John Neoptolemos
- The NIHR Liverpool Pancreas Biomedical Research Unit, Liverpool, United Kingdom
| | - Eithne Costello
- The NIHR Liverpool Pancreas Biomedical Research Unit, Liverpool, United Kingdom
| | - William Greenhalf
- The NIHR Liverpool Pancreas Biomedical Research Unit, Liverpool, United Kingdom
| | - Nick R Lemoine
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Tatjana Crnogorac-Jurcevic
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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Guo Z, Zhang Y, Zou L, Wang D, Shao C, Wang Y, Sun W, Zhang L. A Proteomic Analysis of Individual and Gender Variations in Normal Human Urine and Cerebrospinal Fluid Using iTRAQ Quantification. PLoS One 2015. [PMID: 26222143 PMCID: PMC4519152 DOI: 10.1371/journal.pone.0133270] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Urine and cerebrospinal fluid (CSF) are two important biofluids used for disease biomarker discovery. For differential proteomic analysis, it is essential to evaluate individual and gender variations. In this study, we characterized urinary and CSF proteomes of 14 healthy volunteers with regard to individual and gender variations using 2DLC-MS/MS analysis and 8-plex iTRAQ quantification. A total of 968/512 urinary/CSF proteins were identified, with 406/280 quantified in all individuals. The median inter-individual coefficients of variation (CVs) were 0.262 and 0.183 for urinary and CSF proteomes, respectively. Cluster analysis showed that male and female urinary proteomes exhibited different patterns, though CSF proteome showed no remarkable gender differences. In comparison with CSF proteome, urinary proteome showed higher individual variation. Further analysis revealed that individual variation was not correlated with protein abundance. The minimum sample size for proteomic analysis with a 2-fold change was 10 (4/5 for males/females using iTRAQ quantification) for urinary or 8 for CSF proteome. Intracellular proteins leaked from exfoliative cells tended to have higher CVs, and extracellular proteins secreted from urinary tract or originating from plasma tended to have lower CVs. The above results might be beneficial for differential proteomic analysis and biomarker discovery.
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Affiliation(s)
- Zhengguang Guo
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Yang Zhang
- Department of Neurosurgery/China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
| | - Lili Zou
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Danqi Wang
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Chen Shao
- National Key Laboratory of Medical Molecular Biology, Department of Physiology and Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
| | - Yajie Wang
- Core Laboratory for Clinical Medical Research, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
- Department of Clinical Laboratory Diagnosis, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
| | - Wei Sun
- Core Facility of Instrument, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing, China, 100005
- * E-mail: (WS); (LZ)
| | - Liwei Zhang
- Department of Neurosurgery/China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, 6 Tian Tan Xi Li, Beijing, China, 100050
- * E-mail: (WS); (LZ)
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22
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Adeola HA, Soares NC, Paccez JD, Kaestner L, Blackburn JM, Zerbini LF. Discovery of novel candidate urinary protein biomarkers for prostate cancer in a multiethnic cohort of South African patients via label-free mass spectrometry. Proteomics Clin Appl 2015; 9:597-609. [PMID: 25708745 DOI: 10.1002/prca.201400197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/29/2015] [Accepted: 02/18/2015] [Indexed: 01/10/2023]
Abstract
PURPOSE Improvement in diagnostic accuracy of prostate cancer (PCa) progression using MS-based methods to analyze biomarkers in our African, Caucasian, and Mixed Ancestry patients can advance early detection and treatment monitoring. EXPERIMENTAL DESIGN MS-based proteomic analysis of pooled (N = 36) and individual samples (N = 45) of PCa, benign prostatic hyperplasia, normal healthy controls, and patients with other uropathies was used to identify differences in proteomics profile. Samples were analyzed for potential biomarkers and proteome coverage in African, Caucasian, and Mixed Ancestry PCa patients. RESULTS A total of 1102 and 5595 protein groups and nonredundant peptides, respectively, were identified in the pooling experiments (FDR = 0.01). Twenty potential biomarkers in PCa were identified and fold differences ± 2SD were observed in 17 proteins using intensity-based absolute quantification. Analysis of 45 individual samples yielded 1545 and 9991 protein groups and nonredundant peptides, respectively. Seventy-three (73) proteins groups, including existing putative PCa biomarkers, were found to be potential biomarkers of PCa by label-free quantification and demonstrated ethnic trends within our PCa cohort. CONCLUSION AND CLINICAL RELEVANCE Urinary proteomics is a promising route to PCa biomarker discovery and may serve as source of ethnic-related biomarkers of PCa.
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Affiliation(s)
- Henry A Adeola
- International Centre for Genetic Engineering and Biotechnology, University of Cape Town, Cape Town, South Africa.,Faculty of Health Sciences, Division of Medical Biochemistry, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nelson C Soares
- Faculty of Health Sciences, Division of Medical Biochemistry, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Juliano D Paccez
- International Centre for Genetic Engineering and Biotechnology, University of Cape Town, Cape Town, South Africa.,Faculty of Health Sciences, Division of Medical Biochemistry, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Lisa Kaestner
- Urology Department, Grootes Schuur Hospital, Cape Town, South Africa
| | - Jonathan M Blackburn
- Faculty of Health Sciences, Division of Medical Biochemistry, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Luiz F Zerbini
- International Centre for Genetic Engineering and Biotechnology, University of Cape Town, Cape Town, South Africa.,Faculty of Health Sciences, Division of Medical Biochemistry, Institute of Infectious Diseases & Molecular Medicine, University of Cape Town, Cape Town, South Africa
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23
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Urinary protein biomarker database: a useful tool for biomarker discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 845:195-203. [PMID: 25355582 DOI: 10.1007/978-94-017-9523-4_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
An open-access biomarker database offers a convenient tool for researchers to acquire existing knowledge about proteins and diseases by simply querying its Web site. Biologists can use the biomarker database to assess the confidence and disease specificity of their own research results by cross-study comparison, and bioinformaticians can use it to discover new relationships between diseases and proteins by reanalyzing data via new strategies. This chapter introduces the urinary protein biomarker database, a manually curated database that aim to collect all studies of urinary protein biomarkers from published literature. In the current stage, this database includes very few disease-specific biomarker candidates that have been reported by multiple studies, reflecting current status in the field of urinary biomarker discovery. We believe that this situation will be improved with the development of technologies and accumulation of data, and a more complete and precise biomarker database will play more important role in future studies.
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Beretov J, Wasinger VC, Schwartz P, Graham PH, Li Y. A standardized and reproducible urine preparation protocol for cancer biomarkers discovery. BIOMARKERS IN CANCER 2014; 6:21-7. [PMID: 25452700 PMCID: PMC4219630 DOI: 10.4137/bic.s17991] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/30/2014] [Accepted: 08/07/2014] [Indexed: 12/11/2022]
Abstract
A suitable and standardized protein purification technique is essential to maintain consistency and to allow data comparison between proteomic studies for urine biomarker discovery. Ultimately, efforts should be made to standardize urine preparation protocols. The aim of this study was to develop an optimal analytical protocol to achieve maximal protein yield and to ensure that this method was applicable to examine urine protein patterns that distinguish disease and disease-free states. In this pilot study, we compared seven different urine sample preparation methods to remove salts, and to precipitate and isolate urinary proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) profiles showed that the sequential preparation of urinary proteins by combining acetone and trichloroacetic acid (TCA) alongside high speed centrifugation (HSC) provided the best separation, and retained the most urinary proteins. Therefore, this approach is the preferred method for all further urine protein analysis.
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Affiliation(s)
- Julia Beretov
- Cancer Care Centre, St George Hospital, Gray St, Kogarah, NSW, Australia. ; St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, NSW, Australia. ; SEALS, Anatomical Pathology, St George Hospital, Gray St, Kogarah, NSW, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Peter Schwartz
- Breast Surgery, St George Private Hospital, South St, Kogarah, NSW, Australia
| | - Peter H Graham
- Cancer Care Centre, St George Hospital, Gray St, Kogarah, NSW, Australia. ; St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Yong Li
- Cancer Care Centre, St George Hospital, Gray St, Kogarah, NSW, Australia. ; St George and Sutherland Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Kensington, NSW, Australia
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25
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Olszowy P, Buszewski B. Urine sample preparation for proteomic analysis. J Sep Sci 2014; 37:2920-8. [PMID: 25132110 DOI: 10.1002/jssc.201400331] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 07/08/2014] [Accepted: 07/18/2014] [Indexed: 12/22/2022]
Abstract
Sample preparation for both environmental and more importantly biological matrices is a bottleneck of all kinds of analytical processes. In the case of proteomic analysis this element is even more important due to the amount of cross-reactions that should be taken into consideration. The incorporation of new post-translational modifications, protein hydrolysis, or even its degradation is possible as side effects of proteins sample processing. If protocols are evaluated appropriately, then identification of such proteins does not bring difficulties. However, if structural changes are provided without sufficient attention then protein sequence coverage will be reduced or even identification of such proteins could be impossible. This review summarizes obstacles and achievements in protein sample preparation of urine for proteome analysis using different tools for mass spectrometry analysis. The main aim is to present comprehensively the idea of urine application as a valuable matrix. This article is dedicated to sample preparation and application of urine mainly in novel cancer biomarkers discovery.
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Affiliation(s)
- Pawel Olszowy
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Torun, Poland; Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University, Torun, Poland
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26
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Kolmeder CA, de Vos WM. Metaproteomics of our microbiome - developing insight in function and activity in man and model systems. J Proteomics 2013; 97:3-16. [PMID: 23707234 DOI: 10.1016/j.jprot.2013.05.018] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 05/13/2013] [Accepted: 05/16/2013] [Indexed: 12/17/2022]
Abstract
We are all colonized by a large microbiome, a complex set of microbes that have intimate associations with us. Culture-based approaches have provided insights in the complexity of the microbial communities living on surfaces inside and outside the body. However, the application of high-throughput sequencing technologies has identified large numbers of community members at both the phylogenetic and the (meta-)genome level. The latter allowed defining a reference set of several millions of mainly bacterial genes and provided the basis for developing approaches to target the activity and function of the human microbiome with proteomic techniques. Moreover, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometers have promoted the field of metaproteomics, the study of the collective proteome of microbial communities. We here review the approaches that have been developed to study the human metaproteomes, focusing on intestinal tract and body fluids. Moreover, we complement these by considering metaproteomic studies in mouse and other model systems offering the option to study single species or simple consortia. Finally, we discuss present and future avenues that may be used to advance the application of metaproteomic approaches to further improve our understanding of the microbes inside and around our body. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Carolin A Kolmeder
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66, FIN-00014 Helsinki, Finland.
| | - Willem M de Vos
- Department of Veterinary Biosciences, University of Helsinki, P.O. Box 66, FIN-00014 Helsinki, Finland; Department of Bacteriology and Immunology, University of Helsinki, P.O. Box 21, FIN-00014 Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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