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Bai Y, Li Y, Tang Z, Hu L, Jiang X, Chen J, Huang S, Wu K, Xu W, Chen C. Urinary proteome analysis of acute kidney injury in post-cardiac surgery patients using enrichment materials with high-resolution mass spectrometry. Front Bioeng Biotechnol 2022; 10:1002853. [PMID: 36177176 PMCID: PMC9513377 DOI: 10.3389/fbioe.2022.1002853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Cardiac surgery-associated acute kidney injury (CSA-AKI) may increase the mortality and incidence rates of chronic kidney disease in critically ill patients. This study aimed to investigate the underlying correlations between urinary proteomic changes and CSA-AKI. Methods: Nontargeted proteomics was performed using nano liquid chromatography coupled with Orbitrap Exploris mass spectrometry (MS) on urinary samples preoperatively and postoperatively collected from patients with CSA-AKI. Gemini C18 silica microspheres were used to separate and enrich trypsin-hydrolysed peptides under basic mobile phase conditions. Differential analysis was conducted to screen out urinary differential expressed proteins (DEPs) among patients with CSA-AKI for bioinformatics. Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis was adopted to identify the altered signal pathways associated with CSA-AKI. Results: Approximately 2000 urinary proteins were identified and quantified through data-independent acquisition MS, and 324 DEPs associated with AKI were screened by univariate statistics. According to KEGG enrichment analysis, the signal pathway of protein processing in the endoplasmic reticulum was enriched as the most up-regulated DEPs, and cell adhesion molecules were enriched as the most down-regulated DEPs. In protein–protein interaction analysis, the three hub targets in the up-regulated DEPs were α-1-antitrypsin, β-2-microglobulin and angiotensinogen, and the three key down-regulated DEPs were growth arrest-specific protein 6, matrix metalloproteinase-9 and urokinase-type plasminogen activator. Conclusion: Urinary protein disorder was observed in CSA-AKI due to ischaemia and reperfusion. The application of Gemini C18 silica microspheres can improve the protein identification rate to obtain highly valuable resources for the urinary DEPs of AKI. This work provides valuable knowledge about urinary proteome biomarkers and essential resources for further research on AKI.
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Affiliation(s)
- Yunpeng Bai
- Center of Scientific Research, Maoming People’s Hospital, Maoming, China
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming, China
| | - Ying Li
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhizhong Tang
- Department of Urology, Maoming People’s Hospital, Maoming, China
| | - Linhui Hu
- Department of Critical Care Medicine, Maoming People’s Hospital, Maoming, China
| | - Xinyi Jiang
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Jingchun Chen
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Sumei Huang
- Center of Scientific Research, Maoming People’s Hospital, Maoming, China
- Department of Emergency, Maoming People’s Hospital, Maoming, China
- Biological Resource Center of Maoming People’s Hospital, Maoming, China
| | - Kunyong Wu
- Center of Scientific Research, Maoming People’s Hospital, Maoming, China
- Biological Resource Center of Maoming People’s Hospital, Maoming, China
| | - Wang Xu
- Department of Intensive Care Unit of Cardiovascular Surgery, Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Critical Care Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Chunbo Chen
- Department of Emergency, Maoming People’s Hospital, Maoming, China
- Department of Critical Care Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Renal Failure Research, Southern Medical University, Guangzhou, China
- *Correspondence: Chunbo Chen, , orcid.org/0000-0001-5662-497X
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Lee H, Kim SI. Review of Liquid Chromatography-Mass Spectrometry-Based Proteomic Analyses of Body Fluids to Diagnose Infectious Diseases. Int J Mol Sci 2022; 23:ijms23042187. [PMID: 35216306 PMCID: PMC8878692 DOI: 10.3390/ijms23042187] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 01/27/2023] Open
Abstract
Rapid and precise diagnostic methods are required to control emerging infectious diseases effectively. Human body fluids are attractive clinical samples for discovering diagnostic targets because they reflect the clinical statuses of patients and most of them can be obtained with minimally invasive sampling processes. Body fluids are good reservoirs for infectious parasites, bacteria, and viruses. Therefore, recent clinical proteomics methods have focused on body fluids when aiming to discover human- or pathogen-originated diagnostic markers. Cutting-edge liquid chromatography-mass spectrometry (LC-MS)-based proteomics has been applied in this regard; it is considered one of the most sensitive and specific proteomics approaches. Here, the clinical characteristics of each body fluid, recent tandem mass spectroscopy (MS/MS) data-acquisition methods, and applications of body fluids for proteomics regarding infectious diseases (including the coronavirus disease of 2019 [COVID-19]), are summarized and discussed.
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Affiliation(s)
- Hayoung Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Seung Il Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute (KBSI), Ochang 28119, Korea;
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon 34113, Korea
- Correspondence:
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Amiri-Dashatan N, Koushki M, Rezaei-Tavirani M. Mass Spectrometry-Based Proteomics Research to Fight COVID-19: An Expert Review on Hopes and Challenges. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:19-34. [PMID: 35005991 DOI: 10.1089/omi.2021.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems perspective remains incomplete. Moreover, there is currently only a limited description of this systemic disease. For precision diagnosis and treatment of SARS-CoV-2, multiomics technologies and systems science research offer significant prospects. This expert review offers a critical analysis of the prospects and challenges of the emerging mass spectrometry-based proteomics approaches to the study of COVID-19 as seen through a systems medicine lens. We also discuss the ways in which proteomics is poised to offer hope for diagnostics and therapeutics innovation on SARS-CoV-2 infection as the disease transitions from a pandemic to an endemic disease, and thus further challenging the health systems and services worldwide in the coming decade. Proteomics is an important high-throughput technology platform to achieve a functional overview of the ways in which COVID-19 changes host biology, and hence, can help identify possible points of entry for innovation in medicines and vaccines, among others.
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Affiliation(s)
- Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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Zhang T, Duran V, Vanarsa K, Mohan C. Targeted urine proteomics in lupus nephritis - a meta-analysis. Expert Rev Proteomics 2021; 17:767-776. [PMID: 33423575 DOI: 10.1080/14789450.2020.1874356] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
BACKGROUND Proteomic approaches are central in biomarker discovery. While mass-spectrometry-based techniques are widely used, novel targeted proteomic platforms have enabled the high-throughput detection of low-abundance proteins in an affinity-based manner. Urine has gained growing attention as an ideal biofluid for monitoring renal disease including lupus nephritis (LN). METHODS Pubmed was screened for targeted proteomic studies of LN urine interrogating ≥1000 proteins. Data from the primary studies were combined and a meta-analysis was performed. Shared proteins elevated in active LN across studies were identified, and relevant pathways were elucidated using ingenuity pathway and gene ontology analysis. Urine proteomic data was cross-referenced against renal single-cell RNAseq data from LN kidneys. RESULTS Two high-throughput targeted proteomic platforms with capacity to interrogate ≥1000 proteins have been used to investigate LN urine. Twenty-three urine proteins were significantly elevated in both studies, including 10 chemokines, and proteins implicated in angiogenesis, and extracellular matrix turnover. Of these, Cathepsin S, CXCL10, FasL, ferritin, macrophage migration inhibitory factor (MIF), and resistin were also significantly elevated within LN kidneys. CONCLUSION Targeted urinary proteomics have uncovered multiple novel biomarkers for LN. Further validation in prospective cohorts and mechanistic studies are warranted to establish their clinical utility.
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Affiliation(s)
- Ting Zhang
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
| | - Valeria Duran
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
| | - Kamala Vanarsa
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
| | - Chandra Mohan
- Department of Biomedical Engineering, University of Houston , Houston, Texas, USA
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Improved isolation strategies to increase the yield and purity of human urinary exosomes for biomarker discovery. Sci Rep 2018; 8:3945. [PMID: 29500443 PMCID: PMC5834546 DOI: 10.1038/s41598-018-22142-x] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/12/2018] [Indexed: 12/13/2022] Open
Abstract
Circulating miRNAs are detected in extracellular space and body fluids such as urine. Circulating RNAs can be packaged in secreted urinary extracellular vesicles (uEVs) and thus protected from degradation. Urinary exosome preparations might contain specific miRNAs, relevant as biomarkers in renal and bladder diseases. Major difficulties in application of uEVs into the clinical environment are the high variability and low reproducibility of uEV isolation methods. Here we used five different methods to isolate uEVs and compared the size distribution, morphology, yield, presence of exosomal protein markers and RNA content of uEVs. We present an optimized ultracentrifugation and size exclusion chromatography approach for highly reproducible isolation for 50-150 nm uEVs, corresponding to the exosomes, from 50 ml urine. We profiled the miRNA content of uEVs and total urine from the same samples with the NanoString platform and validated the data using qPCR. Our results indicate that 18 miRNAs, robustly detected in uEVs were always present in the total urine. However, 15 miRNAs could be detected only in the total urine preparations and might represent naked circulating miRNA species. This is a novel unbiased and reproducible strategy for uEVs isolation, content normalization and miRNA cargo analysis, suitable for biomarker discovery studies.
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Csősz É, Kalló G, Márkus B, Deák E, Csutak A, Tőzsér J. Quantitative body fluid proteomics in medicine - A focus on minimal invasiveness. J Proteomics 2016; 153:30-43. [PMID: 27542507 DOI: 10.1016/j.jprot.2016.08.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/27/2016] [Accepted: 08/08/2016] [Indexed: 01/07/2023]
Abstract
Identification of new biomarkers specific for various pathological conditions is an important field in medical sciences. Body fluids have emerging potential in biomarker studies especially those which are continuously available and can be collected by non-invasive means. Changes in the protein composition of body fluids such as tears, saliva, sweat, etc. may provide information on both local and systemic conditions of medical relevance. In this review, our aim is to discuss the quantitative proteomics techniques used in biomarker studies, and to present advances in quantitative body fluid proteomics of non-invasively collectable body fluids with relevance to biomarker identification. The advantages and limitations of the widely used quantitative proteomics techniques are also presented. Based on the reviewed literature, we suggest an ideal pipeline for body fluid analyses aiming at biomarkers discoveries: starting from identification of biomarker candidates by shotgun quantitative proteomics or protein arrays, through verification of potential biomarkers by targeted mass spectrometry, to the antibody-based validation of biomarkers. The importance of body fluids as a rich source of biomarkers is discussed. SIGNIFICANCE Quantitative proteomics is a challenging part of proteomics applications. The body fluids collected by non-invasive means have high relevance in medicine; they are good sources for biomarkers used in establishing the diagnosis, follow up of disease progression and predicting high risk groups. The review presents the most widely used quantitative proteomics techniques in body fluid analysis and lists the potential biomarkers identified in tears, saliva, sweat, nasal mucus and urine for local and systemic diseases.
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Affiliation(s)
- Éva Csősz
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Gergő Kalló
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Bernadett Márkus
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Eszter Deák
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary; Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - Adrienne Csutak
- Department of Ophthalmology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary
| | - József Tőzsér
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary.
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7
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Hall AM, Vilasi A, Garcia-Perez I, Lapsley M, Alston CL, Pitceathly RDS, McFarland R, Schaefer AM, Turnbull DM, Beaumont NJ, Hsuan JJ, Cutillas PR, Lindon JC, Holmes E, Unwin RJ, Taylor RW, Gorman GS, Rahman S, Hanna MG. The urinary proteome and metabonome differ from normal in adults with mitochondrial disease. Kidney Int 2015; 87:610-22. [PMID: 25207879 DOI: 10.1038/ki.2014.297] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/27/2014] [Accepted: 07/10/2014] [Indexed: 02/08/2023]
Abstract
We studied the extent and nature of renal involvement in a cohort of 117 adult patients with mitochondrial disease, by measuring urinary retinol-binding protein (RBP) and albumin; established markers of tubular and glomerular dysfunction, respectively. Seventy-five patients had the m.3243A>G mutation and the most frequent phenotypes within the entire cohort were 14 with MELAS, 33 with MIDD, and 17 with MERRF. Urinary RBP was increased in 29 of 75 of m.3243A>G patients, whereas albumin was increased in 23 of the 75. The corresponding numbers were 16 and 14, respectively, in the 42 non-m.3243A>G patients. RBP and albumin were higher in diabetic m.3243A>G patients than in nondiabetics, but there were no significant differences across the three major clinical phenotypes. The urine proteome (mass spectrometry) and metabonome (nuclear magnetic resonance) in a subset of the m.3243A>G patients were markedly different from controls, with the most significant alterations occurring in lysosomal proteins, calcium-binding proteins, and antioxidant defenses. Differences were also found between asymptomatic m.3243A>G carriers and controls. No patients had an elevated serum creatinine level, but 14% had hyponatremia, 10% had hypophosphatemia, and 14% had hypomagnesemia. Thus, abnormalities in kidney function are common in adults with mitochondrial disease, exist in the absence of elevated serum creatinine, and are not solely explained by diabetes.
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Affiliation(s)
- Andrew M Hall
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Annalisa Vilasi
- Laboratory of Mass Spectrometry and Proteomics, Institute of Protein Biochemistry-CNR, Naples, Italy
| | - Isabel Garcia-Perez
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Marta Lapsley
- South West Thames Institute for Renal Research, St Helier University Hospitals, Surrey, UK
| | - Charlotte L Alston
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Robert D S Pitceathly
- Medical Research Council Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, University College London Institute of Neurology, London, UK
| | - Robert McFarland
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew M Schaefer
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Nick J Beaumont
- Division of Medicine, Institute for Liver & Digestive Health, University College London, London, UK
| | - Justin J Hsuan
- Division of Medicine, Institute for Liver & Digestive Health, University College London, London, UK
| | - Pedro R Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary, University of London, London, UK
| | - John C Lindon
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Elaine Holmes
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Robert J Unwin
- UCL Centre for Nephrology, Royal Free Hospital, London, UK
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Grainne S Gorman
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | | | - Michael G Hanna
- Medical Research Council Centre for Neuromuscular Diseases, National Hospital for Neurology and Neurosurgery, University College London Institute of Neurology, London, UK
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Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Rev Mol Diagn 2014; 12:343-59. [DOI: 10.1586/erm.12.31] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Marshall RP, Simpson JK, Lukey PT. Strategies for biomarker discovery in fibrotic disease. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1079-87. [PMID: 23376113 DOI: 10.1016/j.bbadis.2013.01.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 01/18/2013] [Accepted: 01/22/2013] [Indexed: 01/06/2023]
Abstract
The discovery and development of biomarkers for fibrotic diseases have potential utility in clinical decision-making as well as in pharmaceutical research and development. This review describes strategies for identifying diagnostic, prognostic and theranostic biomarkers. A range of technologies and platforms for biomarker discovery are highlighted, including several with specific relevance for fibrosis. Some challenges specific to fibrotic diseases are outlined including; benchmarking biomarkers against imperfect clinical measures of fibrosis, the complexity resulting from diverse aetiologies and target organs, and the availability of samples (including biopsy) from well-characterised patients with fibrotic disease. To overcome these challenges collaboration amongst clinical specialities as well as between academia and industry is essential. This article is part of a Special Issue entitled: Fibrosis: Translation of basic research to human disease.
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Affiliation(s)
- Richard P Marshall
- Fibrosis Discovery Performance Unit, GlaxoSmithKline R&D, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK.
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Bai Y, Liu W, Guo Q, Zou Y. Screening for urinary biomarkers of steroid-resistant nephrotic syndrome in children. Exp Ther Med 2012; 5:860-864. [PMID: 23403919 PMCID: PMC3570142 DOI: 10.3892/etm.2012.875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
The present study aimed to screen for urinary biomarkers of steroid-resistant nephrotic syndrome (SRNS) in children. These biomarkers were divided into three groups, the control, the steroid-sensitive nephrotic syndrome (SSNS) and the SRNS groups, which were composed of 45, 32 and 9 children, respectively. Urine samples were obtained and analyzed using Au-chips. Compared with the control group, the peak intensities of four proteins, measured using mass-to-charge ratios, were significantly increased in the primary nephrotic syndrome (PNS; SSNS and SRNS combined) group (P<0.01). The intensity of three and one peaks increased significantly in the SSNS and SRNS groups, respectively, compared with the control (P<0.01). Compared with the SRNS group, the intensity of one protein peak increased in the SSNS group (P<0.01). The diagnostic model was established based on these four protein peaks. The sensitivity and specificity of the model were 88.89 and 93.75%, respectively. Four differentially expressed proteins may consequently serve as urinary biomarkers for SRNS in children.
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Affiliation(s)
- Yongqi Bai
- Department of Pediatrics, Affiliated Hospital of Luzhou Medical College, Luzhou, Sichuan 646000, P.R. China
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Alam-Faruque Y, Huntley RP, Khodiyar VK, Camon EB, Dimmer EC, Sawford T, Martin MJ, O'Donovan C, Talmud PJ, Scambler P, Apweiler R, Lovering RC. The impact of focused Gene Ontology curation of specific mammalian systems. PLoS One 2011; 6:e27541. [PMID: 22174742 PMCID: PMC3235096 DOI: 10.1371/journal.pone.0027541] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/19/2011] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED The Gene Ontology (GO) resource provides dynamic controlled vocabularies to provide an information-rich resource to aid in the consistent description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). System-focused projects, such as the Renal and Cardiovascular GO Annotation Initiatives, aim to provide detailed GO data for proteins implicated in specific organ development and function. Such projects support the rapid evaluation of new experimental data and aid in the generation of novel biological insights to help alleviate human disease. This paper describes the improvement of GO data for renal and cardiovascular research communities and demonstrates that the cardiovascular-focused GO annotations, created over the past three years, have led to an evident improvement of microarray interpretation. The reanalysis of cardiovascular microarray datasets confirms the need to continue to improve the annotation of the human proteome. AVAILABILITY GO ANNOTATION DATA IS FREELY AVAILABLE FROM: ftp://ftp.geneontology.org/pub/go/gene-associations/
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Affiliation(s)
| | - Rachael P. Huntley
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Varsha K. Khodiyar
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Evelyn B. Camon
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Emily C. Dimmer
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Tony Sawford
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Maria J. Martin
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Claire O'Donovan
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Philippa J. Talmud
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Peter Scambler
- Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom
| | - Rolf Apweiler
- EMBL-European Bioinformatics Institute, Hinxton, Cambridge, United Kingdom
| | - Ruth C. Lovering
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London, London, United Kingdom
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