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Biomarkers in Urolithiasis. Urol Clin North Am 2023; 50:19-29. [DOI: 10.1016/j.ucl.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Proteomic analysis of inhibitory protein profiles in the urine of children with nephrolithiasis: implication for disease prevention. Int Urol Nephrol 2022; 54:2783-2788. [PMID: 35879498 DOI: 10.1007/s11255-022-03310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/17/2022] [Indexed: 10/16/2022]
Abstract
PURPOSE In this study we aimed to screen for the presence of biomarkers that are downregulated in children with nephrolithiasis (RS) compared to healthy controls (HC) using a proteomic approach. We hypothesized that RS and HC would display unique inhibitory protein profiles that could be used for comparative pathway analysis. METHODS This is a prospective, controlled, pilot study of pooled urine from RS (N = 30, 24 females, mean age 12.95 ± 4.03 years) versus age- and gender-matched HC, using liquid chromatography-mass spectrometry. The criteria for protein selection were: (1) patient/control abundance ratio of < 0.5; and (2) ≤ 0.05 p-value for the Fisher's Exact Test. Results were confirmed by ELISA testing in individual samples. RESULTS 67 proteins were downregulated in RS group, and 17 of those were significantly different compared to controls. Of those seventeen proteins, five (two actins, annexin A5, keratin 6B, and serpin B4) were completely absent in the urine of stone patients but were found in controls. The remaining twelve proteins were significantly less abundant in the patient's urine compared to healthy controls. Protein-protein interaction modeling of significant proteins identified syndecan-1 as the key node, a protein associated with adhesion pathways. ELISA analysis by subgroups showed statistically significant difference in the urinary excretion of osteopontin (5.1 ± 3.22 ng/mg creatinine vs 14.1 ± 9.5 ng/mg creatinine, p = 0.046) between stone patients with hypocitraturia and controls. Urinary osteopontin concentration was positively correlated with urinary citrate excretion (r = 0.417, p = 0.03). CONCLUSIONS Children with RS have a different urinary inhibitory polypeptide profile compared to HC. Decreased urinary excretion of these proteins indicates their potential inhibitory role in renal stone formation, especially of the adhesion phase. Lower concentration of urinary osteopontin in children with nephrolithiasis and hypocitraturia suggests its potential involvement in the pathogenesis of this disease. Further characterization of these proteins in a larger sample is imperative.
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Brewin A, Sriprasad S, Somani BK. Role of urinary biomarkers for diagnosis and prognosis of kidney stone disease. Curr Opin Urol 2021; 31:71-79. [PMID: 33394608 DOI: 10.1097/mou.0000000000000856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW Urinary biomarkers such as neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1) and N-acetyl-B-D-glucosamindase (NAG) are recognised as being useful for the detection of kidney tubular damage but their role in the diagnosis and prognosis of kidney stone disease (KSD) is still unknown. To clarify this, we performed a systematic review of literature in accordance with Cochrane methodology from inception to September 2020. RECENT FINDINGS Twelve studies were included and a variety of urinary biomarkers (KIM-1, NGAL, NAG, proteins/peptides, cytokines, CA19-9) were measured in a total of 998 patients with KSD. Despite some contradicting studies, majority of the biomarkers studied showed a significant rise in patients with KSD compared to healthy controls, with levels decreasing after their surgical management, noticed as early as 4 h postprocedure. There was limited evidence of correlation with stone burden and elevated levels were also associated with hydronephrosis and superimposed infections. SUMMARY Urinary biomarkers could be used in the diagnosis, prognosis and stone-treatment response in patients with KSD. However, as novel indicators, they may not be reliable as the sole diagnostic or prognostic tool for KSD as they are readily confounded by other causes of kidney injury. Further studies are needed to determine their ability to separate KSD from other causes of obstructive uropathy and acute renal injury.
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Affiliation(s)
- Anna Brewin
- Clinical Fellow in Urology, University Hospital Southampton NHS Trust, Southampton
| | - Sheshadri Sriprasad
- Institute of Medical Sciences, Canterbury Christ Church University, Kent, UK
| | - Bhaskar K Somani
- Clinical Fellow in Urology, University Hospital Southampton NHS Trust, Southampton
- KMC Manipal, Manipal Academy of Higher Education (MAHE), Karnataka, India
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iTRAQ-Based Comparative Proteomics Analysis of Urolithiasis Rats Induced by Ethylene Glycol. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6137947. [PMID: 32509863 PMCID: PMC7246402 DOI: 10.1155/2020/6137947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/12/2020] [Accepted: 04/23/2020] [Indexed: 11/18/2022]
Abstract
Nephrolithiasis is a frequent chronic urological condition with a high prevalence and recurrence rate. Proteomics studies on urolithiasis rat models are highly important in characterizing the pathophysiology of kidney stones and identifying potential approaches for preventing and treating kidney stones. The isobaric tags for relative and absolute quantification (iTRAQ) were performed to identify differentially expressed proteins (DEPs) in the kidney between urolithiasis rats and control rats. The results showed that 127 DEPs (85 upregulated and 42 downregulated) were identified in urolithiasis and control rats. The functions of DEPs were predicted by Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein-protein interaction (PPI) network analysis. The expression of four upregulated proteins (Tagln, Akr1c9, Spp1, and Fbn1) and four downregulated proteins (Hbb, Epb42, Hmgcs2, and Ca1) were validated by parallel reaction monitoring (PRM). Proteomics studies of ethylene glycol-induced urolithiasis rat models using iTRAQ and PRM helped to elucidate the molecular mechanism governing nephrolithiasis and to identify candidate proteins for the treatment of kidney stones.
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Urinary proteome in inherited nephrolithiasis. Urolithiasis 2018; 47:91-98. [DOI: 10.1007/s00240-018-01104-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/08/2018] [Indexed: 12/18/2022]
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Kovacevic L, Caruso JA, Lu H, Kovacevic N, Lakshmanan Y, Carruthers NJ, Goldfarb DS. Urine proteomic profiling in patients with nephrolithiasis and cystinuria. Int Urol Nephrol 2018; 51:593-599. [PMID: 30519981 DOI: 10.1007/s11255-018-2044-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 11/23/2018] [Indexed: 01/19/2023]
Abstract
PURPOSE The purpose of the study was to assess the differences in the concentration and function of urinary proteins between patients with cystine stones (CYS) and healthy controls (HC). We postulated that CYS and HC groups would demonstrate different proteomic profiles. METHODS A pilot study was performed comparing urinary proteomes of 10 patients with CYS and 10 age- and gender-matched HC, using liquid chromatography-mass spectrometry. Proteins which met the selection criteria (i) ≥ 2 unique peptide identifications; (ii) ≥ twofold difference in protein abundance; and (iii) ≤ 0.05 p value for the Fisher's Exact Test were analyzed using Gene Ontology classifications. RESULTS Of the 2097 proteins identified by proteomic analysis, 398 proteins were significantly different between CYS and HC. Of those, 191 were involved in transport processes and 61 in inflammatory responses. The majority were vesicle-mediated transport proteins (78.5%), and 1/3 of them were down-regulated; of those, 12 proteins were involved in endosomal transport (including 6 charged multivesicular body proteins (CHMP) and 3 vacuolar sorting-associated proteins) and 9 in transmembrane transport. Myosin-2 and two actin-related proteins were significantly up-regulated in the vesicle-mediated transport group. CONCLUSION We provide proteomic evidence of impaired endocytosis, dysregulation of actin and myosin cytoskeleton, and inflammation in CYS. Endosomal transport proteins were down-regulated mainly through defective CHMP. These findings may contribute to further understanding of the pathogenesis of CYS, potentially affecting its management.
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Affiliation(s)
- Larisa Kovacevic
- Department of Pediatric Urology, Children's Hospital of Michigan, 3901 Beaubien Blvd, Detroit, MI, 48201, USA.
| | - Joseph A Caruso
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - Hong Lu
- Department of Pediatric Urology, Children's Hospital of Michigan, 3901 Beaubien Blvd, Detroit, MI, 48201, USA
| | - Natalija Kovacevic
- Department of Pediatric Urology, Children's Hospital of Michigan, 3901 Beaubien Blvd, Detroit, MI, 48201, USA
- Vattikuti Urology Institute, Henri Ford Hospital, Detroit, MI, USA
| | - Yegappan Lakshmanan
- Department of Pediatric Urology, Children's Hospital of Michigan, 3901 Beaubien Blvd, Detroit, MI, 48201, USA
| | - Nicholas J Carruthers
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, USA
| | - David S Goldfarb
- Nephrology Division, New York University Langone Medical Center, New York, NY, USA
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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: 51] [Impact Index Per Article: 6.4] [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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Husi H, Skipworth RJE, Cronshaw A, Fearon KCH, Ross JA. Proteomic identification of potential cancer markers in human urine using subtractive analysis. Int J Oncol 2016; 48:1921-32. [PMID: 26984763 DOI: 10.3892/ijo.2016.3424] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 12/27/2015] [Indexed: 11/06/2022] Open
Abstract
Urine is an ideal medium in which to focus diagnostic cancer research due to the non-invasive nature and ease of sampling. Many large-scale proteomic studies have shown that urine is unexpectedly complex. We hypothesised that novel diagnostic cancer biomarkers could be discovered using a comparative proteomic analysis of pre-existing data. We assembled a database of 100 published datasets of 5,620 urinary proteins, as well as 46 datasets of 8,620 non-redundant proteins derived from kidney and blood proteome analyses. The data were then used to either subtract or compare molecules from a novel urinary proteome profiling dataset that we generated. We identified 1,161 unique proteins in samples from either cancer-bearing or healthy subjects. Subtractive analysis yielded a subset of 44 proteins that were found uniquely in urine from cancer patients, 30 of which were linked previously to cancer. In conclusion, this approach is useful in discovering novel biomarkers in tissues where unrelated profiling data is available. Only a limited disease-specific novel dataset is required to define new targets or substantiate previous findings. We have shared this discovery platform in the form of our Large Scale Screening Resource database, accessible through the Proteomic Analysis DataBase portal (www.PADB.org).
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Affiliation(s)
- Holger Husi
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | | | - Andrew Cronshaw
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - Kenneth C H Fearon
- School of Clinical Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
| | - James A Ross
- School of Clinical Sciences, University of Edinburgh, Edinburgh, EH16 4SB, UK
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Kovacevic L, Lu H, Goldfarb DS, Lakshmanan Y, Caruso JA. Urine proteomic analysis in cystinuric children with renal stones. J Pediatr Urol 2015; 11:217.e1-6. [PMID: 26076823 PMCID: PMC4540695 DOI: 10.1016/j.jpurol.2015.04.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/25/2015] [Indexed: 11/16/2022]
Abstract
INTRODUCTION The gene mutations responsible for cystinuria do not fully explain kidney stone activity, suggesting that specific proteins may serve as promoters of cystine precipitation, aggregation or epithelial adherence. In this study we assessed (1) the differences in the urinary proteins between children with cystinuria and kidney stones (CYS) and healthy controls (HC), with particular attention to the fibrosis-related proteins, and (2) the presence of diagnostic biomarkers for CYS. MATERIAL AND METHODS We conducted a pilot study comparing individual urinary proteomes of 2 newly diagnosed children with CYS and 2 age- and gender-matched HC, using liquid chromatography-mass spectrometry. Relative protein abundance was estimated using spectral counting. Proteins of interest in both CYS and HC were selected using the following criteria: i) ≥5 spectral counts; ii) ≥2-fold difference in spectral counts; and iii) ≤0.05 p-value for the Fisher's Exact Test. DISCUSSION This study demonstrates a different urinary polypeptide profile in two children with CYS compared to two HC. Of the 623 proteins identified by proteomic analysis, 180 exhibited at least a 2-fold increased relative abundance in CYS compared to HC. Of these, 39 were involved in response to stress, 26 in response to wounding, 21 in inflammatory response, 18 in immune response, and 4 in cellular response to oxidative stress. 133 proteins were found only in children with CYS, 33 of which met the selection criteria. Of these 33 unique proteins, six are known to be associated with fibrosis pathways (Table). The major limitation of this study is the small number of samples that were analyzed. Validation using highly specific methods such as ELISA is needed. CONCLUSION We provide proteomic evidence of oxidative injury, inflammation, wound healing and fibrosis in two children with CYS. We speculate that oxidative stress and inflammation may cause remodeling via actin and vimentin pathways, leading to fibrosis. Additionally, we identified ITIH and MMP-9 as potential diagnostic biomarkers and novel therapeutic targets in CYS. These proteins merit further investigation.
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Affiliation(s)
- Larisa Kovacevic
- Department of Pediatric Urology, Children's Hospital of Michigan, Detroit, MI, USA.
| | - Hong Lu
- Department of Pediatric Urology, Children's Hospital of Michigan, Detroit, MI, USA
| | - David S Goldfarb
- Nephrology Division, NYU Langone Medical Center, New York, NY, USA
| | - Yegappan Lakshmanan
- Department of Pediatric Urology, Children's Hospital of Michigan, Detroit, MI, USA
| | - Joseph A Caruso
- Proteomic Facility, Wayne State University, Detroit, MI, USA
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Xu C, Shu S, Xia C, Wang P, Sun Y, Xu C, Li C. Mass spectral analysis of urine proteomic profiles of dairy cows suffering from clinical ketosis. Vet Q 2015; 35:133-41. [PMID: 26011147 DOI: 10.1080/01652176.2015.1055352] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Ketosis is an important metabolic disorder in dairy cows during the transition period. The urine proteomics of ketosis has not been investigated using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). OBJECTIVE The aim is to determine differences between urine proteomic profiles of healthy cows and those with clinical ketosis, and facilitate studies of the underlying physiological and biochemical mechanisms that lead to liver pathology in ketosis. ANIMALS AND METHODS We analyzed the urine samples of 20 cows with clinical ketosis (group 1) and 20 control cows (group 2) using SELDI-TOF-MS. RESULTS Thirty-nine peptide peaks differed between both groups. Polypeptides corresponding to 26 of these differential peptide peaks were identified using the SWISS-PROT protein database. We found that the peaks of 11 distinct polypeptides from the urine samples of the ketosis group were significantly reduced, compared with those of the control group as based on the Wilcoxon rank sum test. Among these were VGF (non-acronymic) protein, amyloid precursor protein, serum amyloid A (SAA), fibrinogen, C1INH, apolipoprotein C-III, cystatin C, transthyretin, hepcidin, human neutrophil peptides, and osteopontin. CONCLUSION These proteins may represent novel biomarkers of the metabolic changes that occur in dairy cows with ketosis. Our results will help to better understand the physiological changes and pathogenesis observed in cows with ketosis. CLINICAL IMPORTANCE The SELDI-TOF-MS can be used to understand the physiological and biochemical mechanisms of ketosis and identify biomarkers of the disease.
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Affiliation(s)
- Chuang Xu
- a Department of Veterinary Medicine, College of Animal Science and Veterinary Medicine , Heilongjiang Bayi Agricultural University , Daqing 163319 , China
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Dallas DC, Guerrero A, Parker EA, Robinson RC, Gan J, German JB, Barile D, Lebrilla CB. Current peptidomics: applications, purification, identification, quantification, and functional analysis. Proteomics 2015; 15:1026-38. [PMID: 25429922 PMCID: PMC4371869 DOI: 10.1002/pmic.201400310] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/24/2014] [Indexed: 12/28/2022]
Abstract
Peptidomics is an emerging field branching from proteomics that targets endogenously produced protein fragments. Endogenous peptides are often functional within the body-and can be both beneficial and detrimental. This review covers the use of peptidomics in understanding digestion, and identifying functional peptides and biomarkers. Various techniques for peptide and glycopeptide extraction, both at analytical and preparative scales, and available options for peptide detection with MS are discussed. Current algorithms for peptide sequence determination, and both analytical and computational techniques for quantification are compared. Techniques for statistical analysis, sequence mapping, enzyme prediction, and peptide function, and structure prediction are explored.
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Affiliation(s)
- David C. Dallas
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Andres Guerrero
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Evan A. Parker
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Randall C. Robinson
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Junai Gan
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - J. Bruce German
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Daniela Barile
- Department of Food Science and Technology, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
| | - Carlito B. Lebrilla
- Foods for Health Institute, University of California, Davis, One Shields Avenue, Davis, CA, USA
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA, USA
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Fahmy N, Woo M, Alameldin M, Lee JK, MacDonald K, Goneau LW, Cadieux P, Burton J, Pautler S. Endogenous biotin expression in renal and testicular tumours and literature review. Can Urol Assoc J 2014; 8:268-72. [PMID: 25210551 DOI: 10.5489/cuaj.1810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The aim of this study was to examine endogenous biotin levels in tumour specimens collected from patients with renal and testicular tumours and compare them to the surrounding non-neoplastic surgical margin. METHODS Frozen samples were obtained from the Ontario Tumour Bank. Renal and testicular tumour tissue were included in this study. Normal tissue from the negative surgical margins of each tumour served as a control. Biotin detection in tissue specimens was determined using immunohistochemistry (IHC). RESULTS Specimens collected from 56 patients (36 men and 20 women) were included in this study. Histopathology of the 52 renal tumours included 31 (60%) conventional type RCC, 5 (10%) chromophobe RCC, 5 (10%) papillary RCC, 1 (2%) oncocytoma and 10 (19%) upper tract urothelial carcinoma (UC). The 4 testicular tumours included 1 seminomatous (25%) germ cell tumour and 3 (75%) non seminomatous germ cell tumours. CONCLUSION No biotin signal was perceived in all tested tumour samples. Endogenous biotin expression was detected in the matching non-neoplastic surgical margin of tested renal tissues. This lack of staining may prove to be a valuable tool in future studies.
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Affiliation(s)
- Nader Fahmy
- Division of Urology, Department of Surgery, Western University, London ON
| | - Mark Woo
- Division of Urology, Department of Surgery, Western University, London ON
| | - Mona Alameldin
- Department of Anatomical Pathology, Western University, London ON
| | - Joe King Lee
- Division of Urology, Department of Surgery, Western University, London ON
| | - Kyle MacDonald
- Department of Microbiology and Immunology, Western University, London ON
| | - Lee W Goneau
- Department of Microbiology and Immunology, Western University, London ON
| | - Peter Cadieux
- Department of Microbiology and Immunology, Western University, London ON
| | - Jeremy Burton
- Division of Urology, Department of Surgery, Western University, London ON; ; Department of Microbiology and Immunology, Western University, London ON
| | - Stephen Pautler
- Division of Urology, Department of Surgery, Western University, London ON; ; Division of Surgical Oncology, Department of Oncology, Western University, London ON
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Boonla C, Tosukhowong P, Spittau B, Schlosser A, Pimratana C, Krieglstein K. Inflammatory and fibrotic proteins proteomically identified as key protein constituents in urine and stone matrix of patients with kidney calculi. Clin Chim Acta 2013; 429:81-9. [PMID: 24333391 DOI: 10.1016/j.cca.2013.11.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 11/27/2013] [Accepted: 11/27/2013] [Indexed: 11/19/2022]
Abstract
To uncover whether urinary proteins are incorporated into stones, the proteomic profiles of kidney stones and urine collected from the same patients have to be explored. We employed 1D-PAGE and nanoHPLC-ESI-MS/MS to analyze the proteomes of kidney stone matrix (n=16), nephrolithiatic urine (n=14) and healthy urine (n=3). We identified 62, 66 and 22 proteins in stone matrix, nephrolithiatic urine and healthy urine, respectively. Inflammation- and fibrosis-associated proteins were frequently detected in the stone matrix and nephrolithiatic urine. Eighteen proteins were exclusively found in the stone matrix and nephrolithiatic urine, considered as candidate biomarkers for kidney stone formation. S100A8 and fibronectin, representatives of inflammation and fibrosis, respectively, were up-regulated in nephrolithiasis renal tissues. S100A8 was strongly expressed in infiltrated leukocytes. Fibronectin was over-expressed in renal tubular cells. S100A8 and fibronectin were immunologically confirmed to exist in nephrolithiatic urine and stone matrix, but in healthy urine they were undetectable. Conclusion, both kidney stones and urine obtained from the same patients greatly contained inflammatory and fibrotic proteins. S100A8 and fibronectin were up-regulated in stone-baring kidneys and nephrolithiatic urine. Therefore, inflammation and fibrosis are suggested to be involved in the formation of kidney calculi.
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Affiliation(s)
- Chanchai Boonla
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand.
| | - Piyaratana Tosukhowong
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330 Thailand
| | - Björn Spittau
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schlosser
- Center for Biological Systems Analysis (ZBSA), Core Facility Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Chaowat Pimratana
- Division of Urological Surgery, Khon Kaen Hospital, Khon Kaen 40000 Thailand
| | - Kerstin Krieglstein
- Department of Molecular Embryology, Institute for Anatomy and Cell Biology, University of Freiburg, 79104 Freiburg, Germany.
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The Human Urinary Proteome Fingerprint Database UPdb. INTERNATIONAL JOURNAL OF PROTEOMICS 2013; 2013:760208. [PMID: 24222850 PMCID: PMC3809596 DOI: 10.1155/2013/760208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 08/29/2013] [Indexed: 01/30/2023]
Abstract
The use of human urine as a diagnostic tool has many advantages, such as ease of sample acquisition and noninvasiveness. However, the discovery of novel biomarkers, as well as biomarker patterns, in urine is hindered mainly by a lack of comparable datasets. To fill this gap, we assembled a new urinary fingerprint database. Here, we report the establishment of a human urinary proteomic fingerprint database using urine from 200 individuals analysed by SELDI-TOF (surface enhanced laser desorption ionisation-time of flight) mass spectrometry (MS) on several chip surfaces (SEND, HP50, NP20, Q10, CM10, and IMAC30). The database currently lists 2490 unique peaks/ion species from 1172 nonredundant SELDI analyses in the mass range of 1500 to 150000. All unprocessed mass spectrometric scans are available as ".xml" data files. Additionally, 1384 peaks were included from external studies using CE (capillary electrophoresis)-MS, MALDI (matrix assisted laser desorption/ionisation), and CE-MALDI hybrids. We propose to use this platform as a global resource to share and exchange primary data derived from MS analyses in urinary research.
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Zerefos PG, Aivaliotis M, Baumann M, Vlahou A. Analysis of the urine proteome via a combination of multi-dimensional approaches. Proteomics 2012; 12:391-400. [DOI: 10.1002/pmic.201100212] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 10/06/2011] [Accepted: 11/26/2011] [Indexed: 11/06/2022]
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Moon PG, You S, Lee JE, Hwang D, Baek MC. Urinary exosomes and proteomics. MASS SPECTROMETRY REVIEWS 2011; 30:1185-1202. [PMID: 21544848 DOI: 10.1002/mas.20319] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 07/23/2010] [Accepted: 07/23/2010] [Indexed: 05/30/2023]
Abstract
A number of highly abundant proteins in urine have been identified through proteomics approaches, and some have been considered as disease-biomarker candidates. These molecules might be clinically useful in diagnosis of various diseases. However, none has proven to be specifically indicative of perturbations of cellular processes in cells associated with urogenital diseases. Exosomes could be released into urine which flows through the kidney, ureter, bladder and urethra, with a process of filtration and reabsorption. Urinary exosomes have been recently suggested as alternative materials that offer new opportunities to identify useful biomarkers, because these exosomes secreted from epithelial cells lining the urinary track might reflect the cellular processes associated with the pathogenesis of diseases in their donor cells. Proteomic analysis of such urinary exosomes assists the search of urinary biomarkers reflecting pathogenesis of various diseases and also helps understanding the function of urinary exosomes in urinary systems. Thus, it has been recently suggested that urinary exosomes are one of the most valuable targets for biomarker development and to understand pathophysiology of relevant diseases.
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Affiliation(s)
- Pyong-Gon Moon
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
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Tooker BC, Bowler RP, Orcutt JM, Maier LA, Christensen HM, Newman LS. SELDI-TOF derived serum biomarkers failed to differentiate between patients with beryllium sensitisation and patients with chronic beryllium disease. Occup Environ Med 2011; 68:759-764. [PMID: 21278142 PMCID: PMC4347852 DOI: 10.1136/oem.2010.058966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
BACKGROUND People exposed to beryllium may develop beryllium sensitisation (BeS) and, in some cases, progress to chronic beryllium disease (CBD). OBJECTIVES The objective of this study was to test the ability of proteomic technology to identify patterns of serum protein biomarkers that allow differentiation between BeS and CBD and thus remove the need for invasive bronchoscopic procedures. METHODS Initially, SELDI-TOF methodology and analysis was performed on serum samples from 30 CBD and 31 BeS patients. RESULTS This 'starter set' yielded two distinct biomarker pattern sets with eight candidate proteins. The first set differentiated between BeS and CBD with 83.3% sensitivity and 82.3% specificity, with 10-fold cross-validation of 75% and 79%, respectively. The second set of biomarkers yielded higher sensitivity (90.0%) and higher specificity (90.3%), with 10-fold cross-validation of 71.7% and 82.3%, respectively. Due to its greater sensitivity and specificity, the second set of biomarkers was used as the framework for differentiating between CBD and BeS in a second set of serum samples from 450 patients with BeS and CBD. When this larger set of samples was subjected to the biomarker framework in a blinded fashion, it yielded a sensitivity of 43.53% and a specificity of 38.93%. CONCLUSIONS Due to these low sensitivity and specificity values, we have concluded that, currently, the unique set of SELDI-TOF derived biomarkers does not possess the qualities that would allow it to differentiate between a CBD patient and a BeS patient using serum protein biomarkers. Future refinements in sample collection or proteomic technology may be needed to improve biomarker discovery.
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Affiliation(s)
- B C Tooker
- University of Colorado Denver, Colorado School of Public Health, Division of Allergy and Clinical Immunology, Aurora, CO 80045, USA.
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18
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Wright CA, Howles S, Trudgian DC, Kessler BM, Reynard JM, Noble JG, Hamdy FC, Turney BW. Label-free quantitative proteomics reveals differentially regulated proteins influencing urolithiasis. Mol Cell Proteomics 2011; 10:M110.005686. [PMID: 21474797 PMCID: PMC3149087 DOI: 10.1074/mcp.m110.005686] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Urinary proteins have been implicated as inhibitors of kidney stone formation (urolithiasis). As a proximal fluid, prefiltered by the kidneys, urine is an attractive biofluid for proteomic analysis in urologic conditions. However, it is necessary to correct for variations in urinary concentration. In our study, individual urine samples were normalized for this variation by using a total protein to creatinine ratio. Pooled urine samples were compared in two independent experiments. Differences between the urinary proteome of stone formers and nonstone-forming controls were characterized and quantified using label-free nano-ultraperformance liquid chromatography high/low collision energy switching analysis. There were 1063 proteins identified, of which 367 were unique to the stone former groups, 408 proteins were unique to the control pools, and 288 proteins were identified for comparative quantification. Proteins found to be unique in stone-formers were involved in carbohydrate metabolism pathways and associated with disease states. Thirty-four proteins demonstrated a consistent >twofold change between stone formers and controls. For ceruloplasmin, one of the proteins was shown to be more than twofold up-regulated in the stone-former pools, this observation was validated in individuals by enzyme-linked immunosorbent assay. Moreover, in vitro crystallization assays demonstrated ceruloplasmin had a dose-dependent increase on calcium oxalate crystal formation. Taken together, these results may suggest a functional role for ceruloplasmin in urolithiasis.
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Affiliation(s)
- C A Wright
- Central Proteomics Facility, Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, Roosevelt Drive, University of Oxford, OX3 7BN, UK.
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19
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Good DM, Zürbig P, Argilés A, Bauer HW, Behrens G, Coon JJ, Dakna M, Decramer S, Delles C, Dominiczak AF, Ehrich JHH, Eitner F, Fliser D, Frommberger M, Ganser A, Girolami MA, Golovko I, Gwinner W, Haubitz M, Herget-Rosenthal S, Jankowski J, Jahn H, Jerums G, Julian BA, Kellmann M, Kliem V, Kolch W, Krolewski AS, Luppi M, Massy Z, Melter M, Neusüss C, Novak J, Peter K, Rossing K, Rupprecht H, Schanstra JP, Schiffer E, Stolzenburg JU, Tarnow L, Theodorescu D, Thongboonkerd V, Vanholder R, Weissinger EM, Mischak H, Schmitt-Kopplin P. Naturally occurring human urinary peptides for use in diagnosis of chronic kidney disease. Mol Cell Proteomics 2010; 9:2424-37. [PMID: 20616184 DOI: 10.1074/mcp.m110.001917] [Citation(s) in RCA: 377] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Because of its availability, ease of collection, and correlation with physiology and pathology, urine is an attractive source for clinical proteomics/peptidomics. However, the lack of comparable data sets from large cohorts has greatly hindered the development of clinical proteomics. Here, we report the establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS. All processed data were deposited in an Structured Query Language (SQL) database. This database currently contains 5,010 relevant unique urinary peptides that serve as a pool of potential classifiers for diagnosis and monitoring of various diseases. As an example, by using this source of information, we were able to define urinary peptide biomarkers for chronic kidney diseases, allowing diagnosis of these diseases with high accuracy. Application of the chronic kidney disease-specific biomarker set to an independent test cohort in the subsequent replication phase resulted in 85.5% sensitivity and 100% specificity. These results indicate the potential usefulness of capillary electrophoresis coupled to MS for clinical applications in the analysis of naturally occurring urinary peptides.
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Affiliation(s)
- David M Good
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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20
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Sas DJ, Hulsey TC, Shatat IF, Orak JK. Increasing incidence of kidney stones in children evaluated in the emergency department. J Pediatr 2010; 157:132-7. [PMID: 20362300 DOI: 10.1016/j.jpeds.2010.02.004] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 12/28/2009] [Accepted: 02/03/2010] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To test the hypothesis that there is an increase in the incidence of childhood nephrolithiasis in the state of South Carolina. STUDY DESIGN We analyzed demographic data from a statewide database on incidence of kidney stones from emergency department data and financial charges. Data were compared with population data from the US Census to control for population growth. RESULTS There was a significant increase in the incidence of kidney stones in children between 1996 and 2007. The greatest rate of increase was seen in adolescents, pre-adolescents, and Caucasian children. Infants, toddlers, and African-American children did not show significantly increased incidence in the period. Girls show a growing predominance in our population. The amount of money charged for care of children with kidney stones has gone up >4-fold in our state. CONCLUSION The incidence of kidney stone disease has risen dramatically in the state of South Carolina since 1996. Further studies investigating potential contributing factors are needed to prevent this costly and painful condition.
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Affiliation(s)
- David J Sas
- Division of Pediatric Nephrology, Medical University of South Carolina Children's Hospital, Charleston, SC 29425-6080, USA.
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21
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Ruiz-Romero C, Blanco FJ. Proteomics role in the search for improved diagnosis, prognosis and treatment of osteoarthritis. Osteoarthritis Cartilage 2010; 18:500-9. [PMID: 20060947 DOI: 10.1016/j.joca.2009.11.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 10/21/2009] [Accepted: 11/23/2009] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is the most common rheumatic pathology. It is related to aging and is characterized primarily by cartilage degradation. Despite its high prevalence, the diagnostic methods currently available are limited and lack sensitivity. The focus of this review is the application of proteomic technologies in the search of new biomarkers for improved diagnosis, prognosis and treatment of OA. METHODS This review focuses on the utilization of proteomics in OA biomarker research to enable early diagnosis, improved prognosis and the application of tailored treatments. RESULTS New diagnostic tests for OA are urgently needed and would also promote the development of alternative therapeutic strategies. Considering that OA involves different tissues and complex biological processes, the most promising diagnostic approach would be the study of combinations of biomarkers. New experimental approaches for the identification and validation of OA biomarkers have recently emerged and include proteomic technologies. These techniques allow the simultaneous analysis of multiple markers and become a very powerful tool for both biomarker discovery and validation. CONCLUSIONS Improvements in proteomics technology will undoubtedly lead to advances in characterizing new OA biomarkers and developing alternative therapies. Even so, further work is required to enhance the performance and reproducibility of proteomics tools before they can be routinely used in clinical trials and practice.
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Affiliation(s)
- C Ruiz-Romero
- Laboratorio de Investigación Osteoarticular y del Envejecimiento, Unidad de Proteómica-Nodo Asociado a ProteoRed-(Genoma España), Centro de Investigación Biomédica, Servicio de Reumatología, Complejo Hospitalario Universitario de A Coruña, 15006-A Coruña, Spain
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Bramham K, Mistry HD, Poston L, Chappell LC, Thompson AJ. The non-invasive biopsy--will urinary proteomics make the renal tissue biopsy redundant? QJM 2009; 102:523-38. [PMID: 19553250 DOI: 10.1093/qjmed/hcp071] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Proteomics is a rapidly advancing technique which gives functional insight into gene expression in living organisms. Urine is an ideal medium for study as it is readily available, easily obtained and less complex than other bodily fluids. Considerable progress has been made over the last 5 years in the study of urinary proteomics as a diagnostic tool for renal disease. Advantages over the traditional renal biopsy include accessibility, safety, the possibility of serial sampling and the potential for non-invasive prognostic and diagnostic monitoring of disease and an individual's response to treatment. Urinary proteomics is now moving from a discovery phase in small studies to a validation phase in much larger numbers of patients with renal disease. Whilst there are still some limitations in methodology, which are assessed in this review, the possibility of urinary proteomics replacing the invasive tissue biopsy for diagnosis of renal disease is becoming an increasingly realistic option.
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Affiliation(s)
- K Bramham
- Maternal and Fetal Research Unit, KCL Division of Reproduction and Endocrinology, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.
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Ruiz-Romero C, Blanco FJ. Mitochondrial proteomics and its application in biomedical research. MOLECULAR BIOSYSTEMS 2009; 5:1130-42. [DOI: 10.1039/b906296n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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O'Riordan A, Johnston O, McMorrow T, Wynne K, Maguire P, Hegarty JE, McCormick A, Watson AJ, Cagney G, Gallagher WM, Ryan MP. Identification of Apolipoprotein AI as a serum biomarker of chronic kidney disease in liver transplant recipients, using proteomic techniques. Proteomics Clin Appl 2008; 2:1338-48. [DOI: 10.1002/prca.200780167] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Indexed: 11/06/2022]
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25
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Coon JJ, Zürbig P, Dakna M, Dominiczak AF, Decramer S, Fliser D, Frommberger M, Golovko I, Good DM, Herget-Rosenthal S, Jankowski J, Julian BA, Kellmann M, Kolch W, Massy Z, Novak J, Rossing K, Schanstra JP, Schiffer E, Theodorescu D, Vanholder R, Weissinger EM, Mischak H, Schmitt-Kopplin P. CE-MS analysis of the human urinary proteome for biomarker discovery and disease diagnostics. Proteomics Clin Appl 2008; 2:964. [PMID: 20130789 PMCID: PMC2815342 DOI: 10.1002/prca.200800024] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Indexed: 12/22/2022]
Abstract
Owing to its availability, ease of collection, and correlation with pathophysiology of diseases, urine is an attractive source for clinical proteomics. However, many proteomic studies have had only limited clinical impact, due to factors such as modest numbers of subjects, absence of disease controls, small numbers of defined biomarkers, and diversity of analytical platforms. Therefore, it is difficult to merge biomarkers from different studies into a broadly applicable human urinary proteome database. Ideally, the methodology for defining the biomarkers should combine a reasonable analysis time with high resolution, thereby enabling the profiling of adequate samples and recognition of sufficient features to yield robust diagnostic panels. Capillary electrophoresis coupled to mass spectrometry (CE-MS), which was used to analyze urine samples from healthy subjects and patients with various diseases, is a suitable approach for this task. The database of these datasets compiled from the urinary peptides enabled the diagnosis, classification, and monitoring of a wide range of diseases. CE-MS exhibits excellent performance for biomarker discovery and allows subsequent biomarker sequencing independent of the separation platform. This approach may elucidate the pathogenesis of many diseases, and better define especially renal and urological disorders at the molecular level.
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Affiliation(s)
- Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Petra Zürbig
- Mosaiques diagnostics & therapeutics, Hannover, Germany
| | | | - Anna F. Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow, UK
| | - Stéphane Decramer
- Department of Renal and Cardiac Remodelling, Inserm, U858/I2MR, Toulouse, France
- Université Toulouse III Paul Sabatier, Institut de Médecine Moléculaire de Rangueil, Toulouse, France
- Pediatric Nephrology Unit, Hopital des Enfants, CHU de Toulouse, Toulouse, France
| | - Danilo Fliser
- Department of Nephrology, Hannover Medical School, Hannover, Germany
| | - Moritz Frommberger
- Department of Ecological Chemistry, Helmholtz Center Munich German Research Center for Health and Environment, Neuherberg, Germany
| | - Igor Golovko
- Mosaiques diagnostics & therapeutics, Hannover, Germany
| | - David M. Good
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | - Walter Kolch
- The Beatson Institute for Cancer Research & Sir Henry Wellcome Functional Genomics Facility, University of Glasgow, Glasgow, UK
| | - Ziad Massy
- Departments of Clinical Pharmacology and Nephrology, INSERM, ERI-12, and Amiens University Hospital, UPJV, Amiens, France
| | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Joost P. Schanstra
- Department of Renal and Cardiac Remodelling, Inserm, U858/I2MR, Toulouse, France
- Université Toulouse III Paul Sabatier, Institut de Médecine Moléculaire de Rangueil, Toulouse, France
| | - Eric Schiffer
- Mosaiques diagnostics & therapeutics, Hannover, Germany
| | - Dan Theodorescu
- Department of Urology, University of Virginia, Charlottesville, VA, USA
| | - Raymond Vanholder
- Department of Internal Medicine, University Hospital Ghent, Ghent, Belgium
| | - Eva M. Weissinger
- Department of Hematology, Hemostasis and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Philippe Schmitt-Kopplin
- Department of Ecological Chemistry, Helmholtz Center Munich German Research Center for Health and Environment, Neuherberg, Germany
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26
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Chen WC, Lai CC, Lai CC, Tsai Y, Tsai YH, Lin WY, Tsai FJ. Mass spectroscopic characteristics of low molecular weight proteins extracted from calcium oxalate stones: preliminary study. J Clin Lab Anal 2008; 22:77-85. [PMID: 18200570 DOI: 10.1002/jcla.20214] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
It is believed that boundary compositions of matrix proteins might play a role in stone formation; however, few proteomic studies concerning matrix proteins in urinary stones have been conducted. In this study, we extracted low molecular weight proteins from calcium oxalate stones and measured their characteristic patterns by mass spectroscopy. A total of 10 stones were surgically removed from patients with urolithiasis. Proteins were extracted from the stones and identified by one-dimensional electrophoresis (sodium dodecyl sulfate buffer [SDS]-polyacrylamide gel electrophoresis [SDS-PAGE]). After in-gel digest, samples were analyzed by the surface-enhanced laser desorption ionization-time of flight (SELDI-TOF) technique. The peptide sequences were analyzed from the data of mass spectroscopy. Proteins were identified from Database Search (SwissProt Protein Database; Swiss Institute of Bioinformatics; http://www.expasy.org/sprot) on a MASCOT server (Matrix Science Ltd.; http://www.matrixscience.com). A total of three bands of proteins (27, 18, and 14 kDa) were identified from SDS-PAGE in each stone sample. A database search (SwissProt) on a MASCOT server revealed that the most frequently seen proteins from band 1 (27 kDa) were leukocyte elastase precursor, cathepsin G precursor, azurocidin precursor, and myeloblastin precursor (EC 3.4.21.76) (leukocyte proteinase 3); band 2 (18 kDa) comprised calgranulin B, eosinophil cationic protein precursor, and lysozyme C precursor; band 3 (14 kDa) showed neutrophil defensin 3 precursor, calgranulin A, calgranulin C, and histone H4. The modifications and deamidations found from the mass pattern of these proteins may provide information for the study of matrix proteins. Various lower molecular weight proteins can be extracted from calcium oxalate stones. The characteristic patterns and their functions of those proteins should be further tested to investigate their roles in stone formation.
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Affiliation(s)
- Wen-Chi Chen
- Department of Urology, China Medical University Hospital, Taichung, Taiwan.
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27
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Pugia MJ, Jortani SA, Basu M, Sommer R, Kuo HH, Murphy S, Williamson D, Vranish J, Boyle PJ, Budzinski D, Valdes R, Basu SC. Immunological evaluation of urinary trypsin inhibitors in blood and urine: role of N- & O-linked glycoproteins. Glycoconj J 2007; 24:5-15. [PMID: 17115277 DOI: 10.1007/s10719-006-9009-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Urinary trypsin inhibitors (uTi) suppress serine proteases during inflammation. After liberation from proinhibitors (P-alpha-I and I-alpha-I) by the white blood cell (WBC) response, uTi readily pass through the kidneys into urine. A key uTi, bikunin, is attached to O-linked and N-linked glycoconjugates. Recently, uTi inhibitors, called uristatins, were found to lack the O-linked glycoconjugates. Monoclonal antibodies were produced using purified uristatin and screened for binding differences to uristatin, bikunin, P-alpha-I, and I-alpha-I. Antibody-binding patterns were characterized using immunoaffinity binding onto protein-chip surfaces and analysis by Surface Enhanced Laser Desorption/Ionization mass spectrometry (SELDI), using specimens from patients and from purified uTi standards. Antibodies were developed and used in an enzyme-linked immunosorbent assay (ELISA) method for uTi measurement in urine and plasma specimens. ELISA was performed on specimens from normal, presumed healthy, controls and from patients who had been screened for inflammation using a high sensitivity C-reactive protein (CRP) test and a complete blood count (CBC). Polyclonal antibody against uTi showed cross-reactivity with the Tamm-Horsfall protein (THP) and with proinhibitors. Screening of anti-uTi monoclonal antibodies (Mab) revealed antibodies that did not cross-react with either of the above, thus providing a tool to measure both uristatin and bikunin in urine with Mab 3G5 and in plasma with Mab 5D11. The monoclonal antibody 5D11 cross-reacts with specific N-linked glycoconjugates of uristatin present in plasma. In ca 96% of healthy adults, uTi were present at <12 mg/l in urine and <4 mg/l in plasma. We also found that patients with an inflammation and a CRP of >2.0 mg/l had higher urinary concentrations of uTi than the control population in every subject. Free uristatin and bikunin pass readily into urine and are primarily bound to heavy chains that constitute the proinhibitor form in plasma.
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Affiliation(s)
- Michael J Pugia
- Diagnostic Business Group, Bayer Healthcare LLC, Elkhart, IN, USA
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28
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Wieland BM, Stewart GD, Skipworth RJE, Sangster K, Fearon KCH, Ross JA, Reiman TJ, Easaw J, Mourtzakis M, Kumar V, Pak BJ, Calder K, Filippatos G, Kremastinos DT, Palcic M, Baracos VE. Is There a Human Homologue to the Murine Proteolysis-Inducing Factor? Clin Cancer Res 2007; 13:4984-92. [PMID: 17785548 DOI: 10.1158/1078-0432.ccr-07-0946] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE A tumor-derived proteolysis-inducing factor (PIF) is suggested to be a potent catabolic factor in skeletal muscle of mice and humans. We aimed to establish the clinical significance of PIF in cancer patients and to elucidate its structural features. EXPERIMENTAL DESIGN PIF was detected in human urine using a monoclonal antibody (mAb) and related to clinical outcomes. PIF immunoaffinity-purified using the mAb was purified/separated using reverse-phase high-performance liquid chromatography and two-dimensional electrophoresis. Ten human cancer cell lines were tested for expression of mRNA encoding PIF core peptide. RESULTS PIF immunoreactivity was present in 160 of 262 patients with advanced cancers of the lung, esophagus/stomach, and other organs. In a Kaplan-Meier survival analysis of 181 lung cancer patients, PIF was unrelated to survival; PIF status was also unrelated to skeletal muscle loss confirmed by computed tomography imaging. PIF was seen in 16 of 24 patients with chronic heart failure and thus is not exclusive to malignant disease. In-gel digestion and mass spectrometric analysis of immunoaffinity purified PIF from cancer patients consistently identified human albumin and immunoglobulins. We showed nonspecific binding of purified albumin and immunoglobulins to the anti-PIF mAb, which is thus not a useful tool for PIF detection or purification in humans. Finally, the human PIF core peptide was detected in human cancer cell lines using reverse transcription-PCR and nucleotide sequencing; however, none of the amplified products had a site for the glycosylation critical to the proteolysis-inducing activity of murine PIF. CONCLUSIONS A putative human homologue of murine PIF and its role in human cancer cachexia cannot be verified.
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Affiliation(s)
- Barbara M Wieland
- Departments of Oncology and Chemistry, University of Alberta, Edmonton, Alberta, Canada
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Thongboonkerd V. Recent progress in urinary proteomics. Proteomics Clin Appl 2007; 1:780-91. [PMID: 21136734 DOI: 10.1002/prca.200700035] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Indexed: 11/08/2022]
Abstract
Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Molecular Biology Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. ,
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30
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Junker K, von Eggeling F, Müller J, Steiner T, Schubert J. [Identification of biomarkers and therapeutic targets for renal cell cancer using ProteinChip technology]. Urologe A 2007; 45:305-6, 308, 310-12 passim. [PMID: 16491405 DOI: 10.1007/s00120-006-1001-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In order to understand tumour biology in its complexity, it is necessary to investigate the proteomics in addition to the DNA and RNA level. SELDI-TOF-MS represents a new technology allowing a highly sensitive high-throughput analysis to detect specific protein profiles. In renal cancer, it was possible to define specific protein patterns in serum. Several proteins have been identified, i.e. serum amyloid alpha (SAA). Analysis of tumour tissues leads to a better understanding of tumour biology and provides the basis for differential classification and evaluation of prognosis. Investigation of the proteome concerning therapy results opens up the possibility of assessing downstream effects on the one hand and identifying biomarkers for selection of patients and therapy monitoring on the other hand. This review presents the first results for renal cancer.
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Affiliation(s)
- K Junker
- Klinik für Urologie, Universitätsklinik der FSU, Jena.
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González-Buitrago JM, Ferreira L, Lorenzo I. Urinary proteomics. Clin Chim Acta 2007; 375:49-56. [PMID: 16942764 DOI: 10.1016/j.cca.2006.07.027] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 07/27/2006] [Accepted: 07/27/2006] [Indexed: 10/24/2022]
Abstract
Protein measurement in urine has been used for many years for the diagnosis and monitoring of renal disease. The pattern of urinary protein excretion can be used to identify the cause of the disease and to classify proteinuria. In recent years, proteomics has proven to be a powerful tool in investigation and clinical medicine. Proteomics employs a protein separation method and the identification of proteins using mass spectrometry. One of the objectives of clinical proteomics is the identification of biological markers of disease. To accomplish this, it is necessary to have a normal proteome of the medium in question, which in our case is urine. Comparison of the normal urinary proteome with the urinary proteome from patients with a defined disease can detect proteins expressed differentially from one another. The aim of this review is to present the situation of urinary proteomics, putting special emphasis on its application in the diagnosis of glomerular diseases, renal allograft rejection, urological cancers and urolithiasis.
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Abstract
The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.
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Affiliation(s)
- Shen Hu
- School of Dentistry, Division of Oral Biology and Medicine, Dental Research Institute, University of California, Los Angeles, CA 90095, USA.
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Abstract
Proteomic technologies are used with increasing frequency in the renal community. In this review, we highlight the use in renal research of a number of available techniques including two-dimensional gel electrophoresis, liquid chromatography/mass spectrometry, surface-enhanced laser desorption/ionization, capillary electrophoresis/mass spectrometry, and antibody and tissue arrays. These techniques have been used to identify proteins or changes in proteins specific to regions of the kidney or associated with renal diseases or toxicity. They have also been used to examine protein expression changes and posttranslational modifications of proteins during signaling. A number of studies have used proteomic methodologies to look for diagnostic biomarkers in body fluids. The rapid rate of development of the technologies along with the combination of classic physiological and biochemical techniques with proteomics will enable new discoveries.
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Affiliation(s)
- Michael G Janech
- Medical University of South Carolina, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29425-2220, USA
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O'Riordan E, Gross SS, Goligorsky MS. Technology Insight: renal proteomics--at the crossroads between promise and problems. ACTA ACUST UNITED AC 2006; 2:445-58. [PMID: 16932479 DOI: 10.1038/ncpneph0241] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2005] [Accepted: 03/23/2006] [Indexed: 01/07/2023]
Abstract
Knowledge of the human genome has fertilized research in the embryonic field of proteomics. The aim of this Review is to examine the recent application of emerging proteomic technologies to diagnosis of renal disease. We discuss the roles, efficacy and diagnostic potential of different proteomic approaches, focusing on current difficulties and potential solutions. Our rudimentary knowledge of the healthy human urine proteome is described, as are studies that have sought to use the urinary proteome as a tool for diagnosis of renal disease. Vignettes of renal proteome are also presented. The integral role of bioinformatics, and the need for standardized sample preservation and reporting of results, are discussed.
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Affiliation(s)
- Edmond O'Riordan
- Department of Medicine, Renal Institute and Division of Nephrology, New York Medical College, Valhalla, NY 10595, USA.
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Lammi MJ, Häyrinen J, Mahonen A. Proteomic analysis of cartilage- and bone-associated samples. Electrophoresis 2006; 27:2687-701. [PMID: 16739228 DOI: 10.1002/elps.200600004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The skeleton of the human body is built of cartilage and bone, which are tissues that contain extensive amounts of extracellular matrix (ECM). In bone, inorganic mineral hydroxyapatite forms 50-70% of the whole weight of the tissue. Although the organic matrix of bone consists of numerous proteins, 90% of it is composed of type I collagen. In cartilage, ECM forms a major fraction of the tissue, type II collagen and aggrecans being the most abundant macromolecules. It is obvious that the high content of ECM components causes analytical problems in the proteomic analysis of cartilage and bone, analogous to those in the analysis of low-abundance proteins present in serum. The massive contents of carbohydrates present in cartilage proteoglycans, and hydroxyapatite in bone, further complicate the situation. However, the development of proteomic tools makes them more and more tempting also for research of musculoskeletal tissues. Application of proteomic techniques to the research of chondrocytes, osteoblasts, osteocytes, and osteoclasts in cell cultures can immediately benefit from the present knowledge. Here we make an overview to previous proteomic research of cartilage- and bone-associated samples and evaluate the future prospects of applying proteomic techniques to investigate key events, such as cellular signal transduction, in cartilage- and bone-derived cells.
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Affiliation(s)
- Mikko J Lammi
- Department of Anatomy, Institute of Biomedicine, University of Kuopio, Finland.
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Abstract
PURPOSE OF REVIEW In this review we discuss the key role renal proteins appear to play during initiation and growth of renal stones. RECENT FINDINGS Specific macromolecules have been identified in urine that can regulate crystal nucleation, growth, aggregation, and adhesion to renal cells. Many are incorporated into the matrix of crystals while they grow, including urinary prothrombin fragment 1, thereby increasing crystal susceptibility to degradation by cellular proteases. None of these macromolecular inhibitors appears to be quantitatively decreased in the urine of stone formers, although functional deficiencies thought due to abnormal glycosylation have been implicated, especially in the case of Tamm Horsfall protein. Increasing information is available on the nature and expression of crystal binding molecules on the renal cell surface, and they appear to be maximally expressed in response to stressful stimuli. Studies that employ atomic force microscopy and knockout mice are now being used to further clarify macromolecule-crystal interactions. SUMMARY The exact series of events that transform supersaturation to crystal formation and renal stones are poorly defined. Multiple anchored and soluble renal proteins potentially modulate or even regulate these events. A combination of proteomics and molecular biology seems likely to unravel these critical mediators in the coming years.
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Affiliation(s)
- Vivek Kumar
- Department of Internal Medicine, Division of Nephrology and Hypertension, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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Abdul-Salam VB, Paul GA, Ali JO, Gibbs SR, Rahman D, Taylor GW, Wilkins MR, Edwards RJ. Identification of plasma protein biomarkers associated with idiopathic pulmonary arterial hypertension. Proteomics 2006; 6:2286-94. [PMID: 16493708 DOI: 10.1002/pmic.200500510] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have employed SELDI-TOF MS to screen for differentially expressed proteins in plasma samples from 27 patients with idiopathic pulmonary arterial hypertension (IPAH) and 26 healthy controls. One ion (m/z approximately 8600) that was found to be elevated in IPAH was validated by SELDI-TOF MS analysis of a second and separate set of plasma samples comprising 30 IPAH patients and 19 controls. The m/z 8600 was purified from plasma by sequential ion exchange and reverse-phase chromatographies and SDS-PAGE. It was identified, following trypsin digestion, by MS peptide analysis as the complement component, complement 4a (C4a) des Arg. Plasma levels of C4a des Arg measured by ELISA confirmed that the levels were significantly higher (p < 0.0001) in IPAH patients (2.12 +/- 0.27 microg/mL) compared with normal controls (0.53 +/- 0.05 microg/mL). A cut-off level of 0.6 microg/mL correctly classified 92% of IPAH patients and 80% of controls. Further studies will be needed to determine its performance as a diagnostic biomarker, whether used alone or in combination with other biomarkers. Nevertheless, this study demonstrates that putative biomarkers characteristic of IPAH can be identified using a conjoint SELDI-TOF MS - proteomics approach.
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Bowler RP, Canham ME, Ellison MC. Surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry to identify patients with chronic obstructive pulmonary disease. COPD 2006; 3:41-50. [PMID: 17175664 DOI: 10.1080/15412550500493394] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
There are currently no blood tests to identify the majority of smokers at risk for chronic obstructive pulmonary disease (COPD). We used plasma protein profiles from surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry to identify a panel of protein biomarkers that can distinguish patients with COPD from closely matched controls. Plasma was obtained from 30 COPD subjects and 30 controls matched for age, sex, and smoking history. Plasma protein profiles were generated using Cu2+-immobilized metal affinity capture (IMAC) and strong anion exchanger (Q10) protein chips. Classification and regression tree (CART) analysis identified a panel of 5 biomarkers using the IMAC protein chip that could distinguish COPD patients from controls with sensitivity and specificity of 91.67% and 88.33%, respectively. The 10-fold cross-validation yielded 81.67% sensitivity and 81.67% specificity. This demonstrates the feasibility of using SELDI as a diagnostic test for COPD; however, larger cohorts will be needed to validate these biomarkers and determine their predictive value longitudinally.
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Affiliation(s)
- Russell P Bowler
- Division of Pulmonary and Critical Care, National Jewish Medical and Research Center, 1400 Jackson Street, Room 729b Denver, Colorado 80206, USA.
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Bowley E, Mulvihill E, Howard JC, Pak BJ, Gan BS, O'Gorman DB. A novel mass spectrometry-based assay for GSK-3beta activity. BMC BIOCHEMISTRY 2005; 6:29. [PMID: 16359552 PMCID: PMC1352369 DOI: 10.1186/1471-2091-6-29] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Accepted: 12/16/2005] [Indexed: 11/29/2022]
Abstract
Background As a component of the progression from genomic to proteomic analysis, there is a need for accurate assessment of protein post-translational modifications such as phosphorylation. Traditional kinase assays rely heavily on the incorporation of γ-P32 radiolabeled isotopes, monoclonal anti-phospho-protein antibodies, or gel shift analysis of substrate proteins. In addition to the expensive and time consuming nature of these methods, the use of radio-ligands imposes restrictions based on the half-life of the radionucleotides and pose potential health risks to researchers. With the shortcomings of traditional assays in mind, the aim of this study was to develop a high throughput, non-radioactive kinase assay for screening Glycogen Synthase Kinase-3beta (GSK-3β) activity. Results Synthetic peptide substrates designed with a GSK-3β phosphorylation site were assayed with both recombinant enzyme and GSK-3β immunoprecipitated from NIH 3T3 fibroblasts. A molecular weight shift equal to that of a single phosphate group (80 Da.) was detected by surface enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS) in a GSK-3β target peptide (2B-Sp). Not only was there a dose-dependent response in molecular weight shift to the amount of recombinant GSK-3β used in this assay, this shift was also inhibited by lithium chloride (LiCl), in a dose-dependent manner. Conclusion We present here a novel method to sensitively measure peptide phosphorylation by GSK-3β that, due to the incorporation of substrate controls, is applicable to either purified enzyme or cell extracts. Future studies using this method have the potential to elucidate the activity of GSK-3β in vivo, and to screen enzyme activity in relation to a variety of GSK-3β related disorders.
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Affiliation(s)
- Erin Bowley
- Cell and Molecular Biology Laboratory, Hand and Upper Limb Centre, Lawson Health Research Institute, St. Joseph's Health Centre, London, Ontario, Canada
| | - Erin Mulvihill
- Cell and Molecular Biology Laboratory, Hand and Upper Limb Centre, Lawson Health Research Institute, St. Joseph's Health Centre, London, Ontario, Canada
| | - Jeffrey C Howard
- Cell and Molecular Biology Laboratory, Hand and Upper Limb Centre, Lawson Health Research Institute, St. Joseph's Health Centre, London, Ontario, Canada
| | - Brian J Pak
- Ciphergen Biosystems International Inc., Fremont, California, USA
| | - Bing Siang Gan
- Cell and Molecular Biology Laboratory, Hand and Upper Limb Centre, Lawson Health Research Institute, St. Joseph's Health Centre, London, Ontario, Canada
- Department of Surgery, University of Western Ontario, London, Ontario, Canada
- Department of Physiology and Pharmacology, University of Western Ontario, London, Ontario, Canada
- Department of Medical Biophysics, University of Western Ontario, London, Ontario, Canada
| | - David B O'Gorman
- Cell and Molecular Biology Laboratory, Hand and Upper Limb Centre, Lawson Health Research Institute, St. Joseph's Health Centre, London, Ontario, Canada
- Department of Surgery, University of Western Ontario, London, Ontario, Canada
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O'Riordan E, Goligorsky MS. Emerging studies of the urinary proteome: the end of the beginning? Curr Opin Nephrol Hypertens 2005; 14:579-85. [PMID: 16205479 DOI: 10.1097/01.mnh.0000168425.60729.36] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Urinary proteomics is a rapidly growing field, holding the promise of discovery of biomarkers of various disease processes and elucidation of pathophysiologic mechanisms of disease states. This may be true not only for renal disease but for diseases of other organs and systemic disorders. RECENT FINDINGS Recent advances in separation technologies and rapid, high-throughput, and accurate protein detection and identification now permit rigorous examination of complex biological fluids. This review sketches the progress achieved in recent years and the existing hurdles in describing a normal urinary proteome, its aberrations in pathological conditions, and the search for biomarkers of several renal and non-renal diseases. SUMMARY The first wave of urinary proteomic studies has now arrived and their results are summarized. Future lines of investigation are delineated.
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Affiliation(s)
- Edmond O'Riordan
- Department of Medicine, Renal Research Institute, New York Medical College, Valhalla, NY 10595, USA.
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Gillette MA, Mani DR, Carr SA. Place of pattern in proteomic biomarker discovery. J Proteome Res 2005; 4:1143-54. [PMID: 16083265 DOI: 10.1021/pr0500962] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of pattern in biomarker discovery and clinical diagnosis is examined in its historical context. The use of MS-derived pattern is treated as a logical extension of prior applications of non-MS-derived pattern. Criticisms pertaining to specific technology platforms and analytic methodologies are considered separately from the larger issues of pattern utility and deployment in biomarker discovery. We present a hybrid strategy that marries the desirable attributes of high-information content MS pattern with the capability to obtain identity, and explore the key steps in establishing a data analysis pipeline for pattern-based biomarker discovery.
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Affiliation(s)
- Michael A Gillette
- The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA.
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Affiliation(s)
- Jean-Philippe Lambert
- Ottawa Institute of Systems Biology, University of Ottawa, 451 Smyth Road, Ottawa, Ontario, Canada K1H 8M5
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447475 DOI: 10.1002/cfg.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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