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OMICS in Chronic Kidney Disease: Focus on Prognosis and Prediction. Int J Mol Sci 2021; 23:ijms23010336. [PMID: 35008760 PMCID: PMC8745343 DOI: 10.3390/ijms23010336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease (CKD) patients are characterized by a high residual risk for cardiovascular (CV) events and CKD progression. This has prompted the implementation of new prognostic and predictive biomarkers with the aim of mitigating this risk. The ‘omics’ techniques, namely genomics, proteomics, metabolomics, and transcriptomics, are excellent candidates to provide a better understanding of pathophysiologic mechanisms of disease in CKD, to improve risk stratification of patients with respect to future cardiovascular events, and to identify CKD patients who are likely to respond to a treatment. Following such a strategy, a reliable risk of future events for a particular patient may be calculated and consequently the patient would also benefit from the best available treatment based on their risk profile. Moreover, a further step forward can be represented by the aggregation of multiple omics information by combining different techniques and/or different biological samples. This has already been shown to yield additional information by revealing with more accuracy the exact individual pathway of disease.
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Moran SM, Scott J, Clarkson MR, Conlon N, Dunne J, Griffin MD, Griffin TP, Groarke E, Holian J, Judge C, Wyse J, McLoughlin K, O’Hara PV, Kretzler M, Little MA. The Clinical Application of Urine Soluble CD163 in ANCA-Associated Vasculitis. J Am Soc Nephrol 2021; 32:2920-2932. [PMID: 34518279 PMCID: PMC8806104 DOI: 10.1681/asn.2021030382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/04/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Up to 70% of patients with ANCA-associated vasculitis (AAV) develop GN, with 26% progressing to ESKD. Diagnostic-grade and noninvasive tools to detect active renal inflammation are needed. Urinary soluble CD163 (usCD163) is a promising biomarker of active renal vasculitis, but a diagnostic-grade assay, assessment of its utility in prospective diagnosis of renal vasculitis flares, and evaluation of its utility in proteinuric states are needed. METHODS We assessed a diagnostic-grade usCD163 assay in (1) a real-world cohort of 405 patients with AAV and 121 healthy and 488 non-AAV disease controls; (2) a prospective multicenter study of 84 patients with potential renal vasculitis flare; (3) a longitudinal multicenter cohort of 65 patients with podocytopathy; and (4) a cohort of 29 patients with AAV (with or without proteinuria) and ten controls. RESULTS We established a diagnostic reference range, with a cutoff of 250 ng/mmol for active renal vasculitis (area under the curve [AUC], 0.978). Using this cutoff, usCD163 was elevated in renal vasculitis flare (AUC, 0.95) but remained low in flare mimics, such as nonvasculitic AKI. usCD163's specificity declined in patients with AAV who had nephrotic-range proteinuria and in those with primary podocytopathy, with 62% of patients with nephrotic syndrome displaying a "positive" usCD163. In patients with AAV and significant proteinuria, usCD163 normalization to total urine protein rather than creatinine provided the greatest clinical utility for diagnosing active renal vasculitis. CONCLUSIONS usCD163 is elevated in renal vasculitis flare and remains low in flare mimics. Nonspecific protein leakage in nephrotic syndrome elevates usCD163 in the absence of glomerular macrophage infiltration, resulting in false-positive results; this can be corrected with urine protein normalization.
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Affiliation(s)
- Sarah M. Moran
- Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland,Department of Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Jennifer Scott
- Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland
| | | | | | | | - Matthew D. Griffin
- REMEDI at CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, National University of Ireland, Galway, Ireland,Department of Nephrology, Saolta University Health Care Group, Galway University Hospitals, Galway, Ireland
| | - Tomas P. Griffin
- REMEDI at CÚRAM SFI Centre for Research in Medical Devices, School of Medicine, National University of Ireland, Galway, Ireland,Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group, Galway University Hospitals, Galway, Ireland
| | | | - John Holian
- St Vincent’s University Hospital, Dublin, Ireland
| | - Conor Judge
- Department of Nephrology, Saolta University Health Care Group, Galway University Hospitals, Galway, Ireland,Centre for Endocrinology, Diabetes and Metabolism, Saolta University Health Care Group, Galway University Hospitals, Galway, Ireland
| | - Jason Wyse
- Discipline of Statistics and Information Systems, Trinity College Dublin, Dublin, Ireland
| | | | | | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
| | - Mark A. Little
- Trinity Health Kidney Centre, Trinity College Dublin, Dublin, Ireland,Beaumont Kidney Centre, Dublin, Ireland,Tallaght University Hospital, Dublin, Ireland
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Tailliar M, Schanstra JP, Dierckx T, Breuil B, Hanouna G, Charles N, Bascands JL, Dussol B, Vazi A, Chiche L, Siwy J, Faguer S, Daniel L, Daugas E, Jourde-Chiche N. Urinary Peptides as Potential Non-Invasive Biomarkers for Lupus Nephritis: Results of the Peptidu-LUP Study. J Clin Med 2021; 10:jcm10081690. [PMID: 33920017 PMCID: PMC8071029 DOI: 10.3390/jcm10081690] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/16/2022] Open
Abstract
Background: Lupus nephritis (LN) is a severe manifestation of Systemic Lupus Erythematosus (SLE). The therapeutic strategy relies on kidney biopsy (KB) results. We tested whether urinary peptidome analysis could non-invasively differentiate active from non-active LN. Design: Urinary samples were collected from 93 patients (55 with active LN and 38 with non-active LN), forming a discovery (n = 42) and an independent validation (n = 51) cohort. Clinical characteristics were collected at inclusion and prospectively for 24 months. The urinary peptidome was analyzed by capillary-electrophoresis coupled to mass-spectrometry, comparing active LN to non-active LN, and assessing chronic lesions and response to therapy. The value of previously validated prognostic (CKD273) and differential diagnostic (LN172) signatures was evaluated. Results: Urinary peptides could not discriminate between active and non-active LN or predict early response to therapy. Tubulo-interstitial fibrosis was correlated to the CKD273. The LN172 score identified 92.5% of samples as LN. Few patients developed new-onset CKD. Conclusions: We validated the CKD273 and LN172 classifiers but did not identify a robust signature that could predict active LN and replace KB. The value of urinary peptidome to predict long-term CKD, or renal flares in SLE, remains to be evaluated.
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Affiliation(s)
- Maxence Tailliar
- AP-HM, Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, 13005 Marseille, France; (M.T.); (B.D.)
| | - Joost P. Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Metabolic and Cardiovascular Disease (I2MC), 31432 Toulouse, France; (J.P.S.); (B.B.); (S.F.)
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Tim Dierckx
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium;
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Metabolic and Cardiovascular Disease (I2MC), 31432 Toulouse, France; (J.P.S.); (B.B.); (S.F.)
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
| | - Guillaume Hanouna
- AP-HP, Service de Néphrologie, Hôpital Bichat, DMU VICTOIRE, 75018 Paris, France; (G.H.); (E.D.)
| | - Nicolas Charles
- Centre de Recherche sur l’Inflammation, Université de Paris, INSERM UMRS1149, CNRS ERL8252, Labex INFLAMEX, DHU FIRE, 75890 Paris, France;
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1188-Université de La Réunion, 97490 Saint-Denis, France;
| | - Bertrand Dussol
- AP-HM, Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, 13005 Marseille, France; (M.T.); (B.D.)
- Centre d’Investigation Clinique, CHU Conception, AP-HM, 13005 Marseille, France;
| | - Alain Vazi
- Centre d’Investigation Clinique, CHU Conception, AP-HM, 13005 Marseille, France;
| | - Laurent Chiche
- Médecine Interne, Hôpital Européen, 13003 Marseille, France;
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany;
| | - Stanislas Faguer
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Metabolic and Cardiovascular Disease (I2MC), 31432 Toulouse, France; (J.P.S.); (B.B.); (S.F.)
- Université Toulouse III Paul-Sabatier, 31062 Toulouse, France
- CHU de Toulouse, Service de Néphrologie, 31300 Toulouse, France
| | - Laurent Daniel
- AP-HM, Laboratoire d’Ananatomie Pathologique, Hôpital de la Timone, 13005 Marseille, France;
- Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, INSERM, INRAE, 13005 Marseille, France
| | - Eric Daugas
- AP-HP, Service de Néphrologie, Hôpital Bichat, DMU VICTOIRE, 75018 Paris, France; (G.H.); (E.D.)
- Centre de Recherche sur l’Inflammation, Université de Paris, INSERM UMRS1149, CNRS ERL8252, Labex INFLAMEX, DHU FIRE, 75890 Paris, France;
| | - Noémie Jourde-Chiche
- AP-HM, Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, 13005 Marseille, France; (M.T.); (B.D.)
- Center for CardioVascular and Nutrition Research (C2VN), Aix-Marseille University, INSERM, INRAE, 13005 Marseille, France
- Correspondence:
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Weissinger EM, Basílio-Queirós D, Metzger J, Bieling LM, Ganser A. Proteomics for hematopoietic stem cell transplantation. Expert Rev Proteomics 2020; 17:201-206. [PMID: 32228239 DOI: 10.1080/14789450.2020.1748501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction: After the genomic era, the analysis of the proteome has gained increasing importance. Peptides and/or proteins present in tissue or body fluids can depict health and are prone to change during disease, not only in configuration but also in abundance. Early on, high throughput proteome analysis was implemented in the diagnostic of therapy-linked or induced complications arising after allogeneic hematopoietic stem cell transplantation (HSCT). Several proteomic approaches are currently used in the prediction or diagnosis of acute and/or chronic graft-versus-host disease (GvHD).Areas covered: This review will report on two high throughput proteomics technologies used in the clinical setting to date, namely enzyme-linked-immunosorbent assays (ELISA) for key proteins involved in the pathogenesis of acute GvHD and on capillary electrophoresis coupled on-line to mass spectrometry (CE-MS). Here, we summarize the current data and discuss the strength as well as the limitations of each method and compare the usefulness and practicability in the post-HSCT setting for prediction and diagnosis of acute GvHD.Expert commentary: Both technologies are applied in the clinic and have been tested on several hundred patients after HSCT. The data from both technologies may complement each other in diagnosis of GvHD.
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Affiliation(s)
- Eva M Weissinger
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Debora Basílio-Queirós
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | | | - Lisa M Bieling
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
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Siwy J, Mischak H, Zürbig P. Proteomics and personalized medicine: a focus on kidney disease. Expert Rev Proteomics 2019; 16:773-782. [DOI: 10.1080/14789450.2019.1659138] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Justyna Siwy
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Harald Mischak
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Petra Zürbig
- R & D, Mosaiques Diagnostics GmbH, Hannover, Germany
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Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
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Kanzelmeyer NK, Zürbig P, Mischak H, Metzger J, Fichtner A, Ruszai KH, Seemann T, Hansen M, Wygoda S, Krupka K, Tönshoff B, Melk A, Pape L. Urinary proteomics to diagnose chronic active antibody-mediated rejection in pediatric kidney transplantation - a pilot study. Transpl Int 2018; 32:28-37. [DOI: 10.1111/tri.13363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/18/2018] [Accepted: 10/15/2018] [Indexed: 01/16/2023]
Affiliation(s)
- Nele Kirsten Kanzelmeyer
- Department of Pediatric Nephrology; Hannover Medical School; Hannover Germany
- Integrated Research and Treatment Center Transplantation (IFB-Tx); Hannover Germany
| | | | - Harald Mischak
- Mosaiques Diagnostics; Hannover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | | | - Alexander Fichtner
- Department of Pediatric I; University Children's Hospital; Heidelberg Germany
| | | | - Tomas Seemann
- Department of Pediatrics; Faculty of Medicine in Pilsen; 2nd Medical Faculty and Biomedical Center; University Hospital Motol; Charles University; Prague Czech Republic
| | | | | | - Kai Krupka
- Department of Pediatric I; University Children's Hospital; Heidelberg Germany
| | - Burkhard Tönshoff
- Department of Pediatric I; University Children's Hospital; Heidelberg Germany
| | - Anette Melk
- Department of Pediatric Nephrology; Hannover Medical School; Hannover Germany
- Integrated Research and Treatment Center Transplantation (IFB-Tx); Hannover Germany
| | - Lars Pape
- Department of Pediatric Nephrology; Hannover Medical School; Hannover Germany
- Integrated Research and Treatment Center Transplantation (IFB-Tx); Hannover Germany
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Pletz J, Enoch SJ, Jais DM, Mellor CL, Pawar G, Firman JW, Madden JC, Webb SD, Tagliati CA, Cronin MTD. A critical review of adverse effects to the kidney: mechanisms, data sources, and in silico tools to assist prediction. Expert Opin Drug Metab Toxicol 2018; 14:1225-1253. [PMID: 30345815 DOI: 10.1080/17425255.2018.1539076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The kidney is a major target for toxicity elicited by pharmaceuticals and environmental pollutants. Standard testing which often does not investigate underlying mechanisms has proven not to be an adequate hazard assessment approach. As such, there is an opportunity for the application of computational approaches that utilize multiscale data based on the Adverse Outcome Pathway (AOP) paradigm, coupled with an understanding of the chemistry underpinning the molecular initiating event (MIE) to provide a deep understanding of how structural fragments of molecules relate to specific mechanisms of nephrotoxicity. Aims covered: The aim of this investigation was to review the current scientific landscape related to computational methods, including mechanistic data, AOPs, publicly available knowledge bases and current in silico models, for the assessment of pharmaceuticals and other chemicals with regard to their potential to elicit nephrotoxicity. A list of over 250 nephrotoxicants enriched with, where possible, mechanistic and AOP-derived understanding was compiled. Expert opinion: Whilst little mechanistic evidence has been translated into AOPs, this review identified a number of data sources of in vitro, in vivo, and human data that may assist in the development of in silico models which in turn may shed light on the interrelationships between nephrotoxicity mechanisms.
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Affiliation(s)
- Julia Pletz
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Steven J Enoch
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Diviya M Jais
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Claire L Mellor
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Gopal Pawar
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - James W Firman
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Judith C Madden
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
| | - Steven D Webb
- b Department of Applied Mathematics , Liverpool John Moores University , Liverpool , UK
| | - Carlos A Tagliati
- c Departamento de Análises Clínicas e Toxicológicas , Universidade Federal de Minas Gerais , Belo Horizonte , Brazil
| | - Mark T D Cronin
- a School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Liverpool , UK
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Siwy J, Zürbig P, Argiles A, Beige J, Haubitz M, Jankowski J, Julian BA, Linde PG, Marx D, Mischak H, Mullen W, Novak J, Ortiz A, Persson F, Pontillo C, Rossing P, Rupprecht H, Schanstra JP, Vlahou A, Vanholder R. Noninvasive diagnosis of chronic kidney diseases using urinary proteome analysis. Nephrol Dial Transplant 2018; 32:2079-2089. [PMID: 27984204 DOI: 10.1093/ndt/gfw337] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022] Open
Abstract
Background In spite of its invasive nature and risks, kidney biopsy is currently required for precise diagnosis of many chronic kidney diseases (CKDs). Here, we explored the hypothesis that analysis of the urinary proteome can discriminate different types of CKD irrespective of the underlying mechanism of disease. Methods We used data from the proteome analyses of 1180 urine samples from patients with different types of CKD, generated by capillary electrophoresis coupled to mass spectrometry. A set of 706 samples served as the discovery cohort, and 474 samples were used for independent validation. For each CKD type, peptide biomarkers were defined using statistical analysis adjusted for multiple testing. Potential biomarkers of statistical significance were combined in support vector machine (SVM)-based classifiers. Results For seven different types of CKD, several potential urinary biomarker peptides (ranging from 116 to 619 peptides) were defined and combined into SVM-based classifiers specific for each CKD. These classifiers were validated in an independent cohort and showed good to excellent accuracy for discrimination of one CKD type from the others (area under the receiver operating characteristic curve ranged from 0.77 to 0.95). Sequence analysis of the biomarkers provided further information that may clarify the underlying pathophysiology. Conclusions Our data indicate that urinary proteome analysis has the potential to identify various types of CKD defined by pathological assessment of renal biopsies and current clinical practice in general. Moreover, these approaches may provide information to model molecular changes per CKD.
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Affiliation(s)
| | | | | | - Joachim Beige
- KfH Renal Unit, Department Nephrology, Leipzig and Martin Luther University, Halle/Wittenberg, Germany
| | - Marion Haubitz
- Department of Nephrology, Klinikum Fulda gAG, Fulda, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, RWTH Aachen University Hospital, Aachen, Germany.,School for Cardiovascular Diseases (CARIM), University of Maastricht, Maastricht, The Netherlands
| | - Bruce A Julian
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - David Marx
- Department of Nephrology and Kidney Transplantation, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hanover, Germany.,BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - William Mullen
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alberto Ortiz
- School of Medicine, Jimenez Diaz Foundation Institute for Health Research, Autonomous University of Madrid, Madrid, Spain
| | | | - Claudia Pontillo
- Mosaiques Diagnostics GmbH, Hanover, Germany.,Charite-Universitätsmedizin, Berlin, Germany
| | - Peter Rossing
- Steno Diabetes Center, Gentofte, Denmark.,Faculty of Health, University of Aarhus, Aarhus, Denmark.,Faculty of Health, University of Copenhagen, Copenhagen, Denmark
| | | | - Joost P Schanstra
- Institute of Cardiovascular and Metabolic Disease, French Institute of Health and Medical Research U1048, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Antonia Vlahou
- Division of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Raymond Vanholder
- Nephrology Section, Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium
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Urinary proteomics using capillary electrophoresis coupled to mass spectrometry for diagnosis and prognosis in kidney diseases. Curr Opin Nephrol Hypertens 2018; 25:494-501. [PMID: 27584928 DOI: 10.1097/mnh.0000000000000278] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
PURPOSE OF REVIEW Urine is the most useful of body fluids for biomarker research. Therefore, we have focused on urinary proteomics, using capillary electrophoresis coupled to mass spectrometry, to investigate kidney diseases in recent years. RECENT FINDINGS Several urinary proteomics studies for the detection of various kidney diseases have indicated the potential of this approach aimed at diagnostic and prognostic assessment. Urinary protein biomarkers such as collagen fragments, serum albumin, α-1-antitrypsin, and uromodulin can help to explain the processes involved during disease progression. SUMMARY Urinary proteomics has been used in several studies in order to identify and validate biomarkers associated with different kidney diseases. These biomarkers, with improved sensitivity and specificity when compared with the current gold standards, provide a significant alternative for diagnosis and prognosis, as well as improving clinical decision-making.
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Pontillo C, Mischak H. Urinary peptide-based classifier CKD273: towards clinical application in chronic kidney disease. Clin Kidney J 2017; 10:192-201. [PMID: 28694965 PMCID: PMC5499684 DOI: 10.1093/ckj/sfx002] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Indexed: 12/22/2022] Open
Abstract
Capillary electrophoresis coupled with mass spectrometry (CE-MS) has been used as a platform for discovery and validation of urinary peptides associated with chronic kidney disease (CKD). CKD affects ∼ 10% of the population, with high associated costs for treatments. A urinary proteome-based classifier (CKD273) has been discovered and validated in cross-sectional and longitudinal studies to assess and predict the progression of CKD. It has been implemented in studies employing cohorts of > 1000 patients. CKD273 is commercially available as an in vitro diagnostic test for early detection of CKD and is currently being used for patient stratification in a multicentre randomized clinical trial (PRIORITY). The validity of the CKD273 classifier has recently been evaluated applying the Oxford Evidence-Based Medicine and Southampton Oxford Retrieval Team guidelines and a letter of support for CKD273 was issued by the US Food and Drug Administration. In this article we review the current evidence published on CKD273 and the challenges associated with implementation. Definition of a possible surrogate early endpoint combined with CKD273 as a biomarker for patient stratification currently appears as the most promising strategy to enable the development of effective drugs to be used at an early time point when intervention can still be effective.
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Affiliation(s)
| | - Harald Mischak
- Mosaiques Diagnostics, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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Nkuipou-Kenfack E, Zürbig P, Mischak H. The long path towards implementation of clinical proteomics: Exemplified based on CKD273. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201600104] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/28/2016] [Accepted: 12/22/2016] [Indexed: 12/26/2022]
Affiliation(s)
| | | | - Harald Mischak
- Mosaiques Diagnostics GmbH; Hannover Germany
- BHF Glasgow Cardiovascular Research Centre; University of Glasgow; Glasgow United Kingdom
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Magalhães P, Schanstra JP, Carrick E, Mischak H, Zürbig P. Urinary biomarkers for renal tract malformations. Expert Rev Proteomics 2016; 13:1121-1129. [PMID: 27791437 DOI: 10.1080/14789450.2016.1254555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Renal tract malformations (RTMs) are congenital anomalies of the kidneys and urinary tract, which are the major cause of end-stage renal disease in children. Using immunoassay-based approaches (ELISA, western blot), individual urinary proteins including transforming growth factor β, tumor necrosis factor and monocyte attractant proteins 1 were found to be associated to RTMs. However, only mass spectrometry (MS) based methods leading to the identification of panels of protein-based markers composed of fragments of the extracellular matrix allowed the prediction of progression of RTMs and its complications. Areas covered: In this review, we summarized relevant studies identified in "Pubmed" using the keywords "urinary biomarkers" and "proteomics" and "renal tract malformations" or "hydronephrosis" or "ureteropelvic junction obstruction" or "posterior urethral valves" or "vesicoureteral reflux". These publications represent studies on potential protein-based biomarkers, either individually or combined in panels, of RTMs in human and animal models. Expert commentary: Successful use in the clinic of these protein-based biomarkers will need to involve larger scale studies to reach sufficient power. Improved performance will potentially come from combining immunoassay- and MS-based markers.
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Affiliation(s)
- Pedro Magalhães
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,b Department of Pediatric Nephrology, Hannover Medical School , Hannover , Germany
| | - Joost P Schanstra
- c Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease , Toulouse , France.,d Université Toulouse III Paul-Sabatier , Toulouse , France
| | - Emma Carrick
- e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Harald Mischak
- a Mosaiques Diagnostics GmbH , Hannover , Germany.,e BHF Glasgow Cardiovascular Research Centre , Institute of Cardiovascular and Medical Sciences, University of Glasgow , Glasgow , UK
| | - Petra Zürbig
- a Mosaiques Diagnostics GmbH , Hannover , Germany
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Urinary peptidomics provides a noninvasive humanized readout of diabetic nephropathy in mice. Kidney Int 2016; 90:1045-1055. [DOI: 10.1016/j.kint.2016.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/25/2016] [Accepted: 06/16/2016] [Indexed: 01/31/2023]
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Barrera-Ocampo A, Arlt S, Matschke J, Hartmann U, Puig B, Ferrer I, Zürbig P, Glatzel M, Sepulveda-Falla D, Jahn H. Amyloid-β Precursor Protein Modulates the Sorting of Testican-1 and Contributes to Its Accumulation in Brain Tissue and Cerebrospinal Fluid from Patients with Alzheimer Disease. J Neuropathol Exp Neurol 2016; 75:903-16. [PMID: 27486134 PMCID: PMC5015660 DOI: 10.1093/jnen/nlw065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The mechanisms leading to amyloid-β (Aβ) accumulation in sporadic Alzheimer disease (AD) are unknown but both increased production or impaired clearance likely contribute to aggregation. To understand the potential roles of the extracellular matrix proteoglycan Testican-1 in the pathophysiology of AD, we used samples from AD patients and controls and an in vitro approach. Protein expression analysis showed increased levels of Testican-1 in frontal and temporal cortex of AD patients; histological analysis showed that Testican-1 accumulates and co-aggregates with Aβ plaques in the frontal, temporal and entorhinal cortices of AD patients. Proteomic analysis identified 10 fragments of Testican-1 in cerebrospinal fluid (CSF) from AD patients. HEK293T cells expressing human wild type or mutant Aβ precursor protein (APP) were transfected with Testican-1. The co-expression of both proteins modified the sorting of Testican-1 into the endocytic pathway leading to its transient accumulation in Golgi, which seemed to affect APP processing, as indicated by reduced Aβ40 and Aβ42 levels in APP mutant cells. In conclusion, patient data reflect a clearance impairment that may favor Aβ accumulation in AD brains and our in vitro model supports the notion that the interaction between APP and Testican-1 may be a key step in the production and aggregation of Aβ species.
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Affiliation(s)
- Alvaro Barrera-Ocampo
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Sönke Arlt
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Jakob Matschke
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Ursula Hartmann
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Berta Puig
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Isidre Ferrer
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Petra Zürbig
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Markus Glatzel
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Diego Sepulveda-Falla
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
| | - Holger Jahn
- From the Institute of Neuropathology (AB-O, JM, BP, MG, DS-F), Department of Psychiatry and Psychotherapy (SA, HJ), University Medical Center Hamburg-Eppendorf, Hamburg, Germany, Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany (UH), Institute of Neuropathology, Bellvitge University Hospital, CIBERNED, Hospitalet de Llobregat, University of Barcelona, Spain (IF), Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany (PZ), and Department of Pharmaceutical Sciences, Natura Research Group, Faculty of Natural Sciences, ICESI University, Cali, Colombia (AB-O)
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Mischak H. Pro: urine proteomics as a liquid kidney biopsy: no more kidney punctures! Nephrol Dial Transplant 2016; 30:532-7. [PMID: 25801638 DOI: 10.1093/ndt/gfv046] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
In this article, the benefits of urinary proteomics in comparison with kidney biopsy are discussed. The majority of urinary proteins are generated by the kidney, hence the urinary proteome holds substantial information on the kidney, and assessment of the urinary proteome could be considered a 'liquid biopsy'. The main question is how well the information contained in the urinary proteome can be assessed today, if it is ready to be routinely used, and what are the advantages and possible disadvantages in comparison with current standards. Since chronic kidney disease (CKD) is by far the largest area in nephrology based on the number of patients affected, the focus of this article is on CKD. Substantial progress was made in the last decade in urinary proteomics, and today we have comparable urinary proteome datasets of tens of thousands of subjects available. Clinical proteomics studies in CKD including close to, or even exceeding, 1000 subjects have recently been published, demonstrating a benefit over the current state-of-the-art in diagnosis and especially prognosis. The first large multicentric randomized controlled intervention trial aiming at preventing CKD by employing urinary proteomics-guided intervention has been initiated recently. These data provide ample evidence for the utility and value of urinary proteomics in nephrology. A further consideration is that the purpose of the biopsy, be it 'liquid' or 'solid', is to guide intervention. However, essentially all drug targets are proteins, not microscopic structures. Therefore, obtaining information on the proteome to guide intervention appears to be the most appropriate approach. Presenting more detailed evidence, I argue that urinary proteome analysis can, in most cases, be employed to guide therapeutic intervention, can be repeated multiple times as it is without any direct risk or discomfort and can be considered as a liquid biopsy.
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Affiliation(s)
- Harald Mischak
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK Mosaiques Diagnostics GmbH, Hannover D-30625, Germany
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17
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Jankowski J, Schanstra JP, Mischak H. Body fluid peptide and protein signatures in diabetic kidney diseases. Nephrol Dial Transplant 2016. [PMID: 26209737 DOI: 10.1093/ndt/gfv091] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Body fluid protein-based biomarkers carry the hope of improving patient management in diabetes by enabling more accurate and earlier detection of diabetic kidney disease (DKD), but also of defining the most suitable therapeutic targets. We present the data on some of the best studied individual protein markers in body fluids and conclude that their potential in clinical application for assessing DKD is moderate. Proteome-based approaches aiming at the identification of panels of body fluid biomarkers might be a valid alternative. We discuss the past (first) clinical proteomics studies in DKD, stressing their drawbacks but also the lessons that could be learned from them, as well as the more recent studies that have a potential for actual clinical implementation. We also highlight relevant issues and current problems associated with clinical proteomics from discovery towards application, and give suggestions for solutions that may help guiding proteomic studies, thereby removing some of the current hurdles for implementation of potentially beneficial results.
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Affiliation(s)
- Joachim Jankowski
- Universitätsklinikum RWTH Aachen, Institute of Molecular Cardiovascular Research, Aachen, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institute of Cardiovascular and Metabolic Disease, Toulouse, France Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics & Therapeutics, Hannover, Germany BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, Faculty of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Abstract
Compared to genomics or transcriptomics, proteomics is often regarded as an "emerging technology," i.e., as not having reached the same level of maturity. While the successful implementation of proteomics workflows and technology still requires significant levels of expertise and specialization, great strides have been made to make the technology more powerful, streamlined and accessible. In 2014, two landmark studies published the first draft versions of the human proteome.We aim to provide an introduction specifically into the background of mass spectrometry (MS)-based proteomics. Within the field, mass spectrometry has emerged as a core technology. Coupled to increasingly powerful separations and data processing and bioinformatics solution, it allows the quantitative analysis of whole proteomes within a matter of days, a timescale that has made global comparative proteome studies feasible at last. We present and discuss the basic concepts behind proteomics mass spectrometry and the accompanying topic of protein and peptide separations, with a focus on the properties of datasets emerging from such studies.
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19
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Kwasnik A, Tonry C, Ardle AM, Butt AQ, Inzitari R, Pennington SR. Proteomes, Their Compositions and Their Sources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:3-21. [DOI: 10.1007/978-3-319-41448-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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20
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Reich HN, Sabelnykova VY, Boutros PC. Matching Kidneys and Urines: Establishing Noninvasive Surrogates of Intrarenal Events in Primary Glomerulonephritis. Semin Nephrol 2015. [PMID: 26215863 DOI: 10.1016/j.semnephrol.2015.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Kidney biopsy is the gold standard procedure for providing diagnostic and prognostic information for patients with glomerular-based diseases, however, the utility of this procedure for assessing longitudinal disease activity is limited. The intense search for noninvasive biomarkers of kidney disease activity and injury is driven in large part by the inherent risks of the kidney biopsy procedure and limited information derived from the morphologic description of biopsy findings. Furthermore, gaps in our understanding of the core intrarenal molecular processes underlying the development and progression of glomerular-based diseases has limited the development of effective targeted therapy. In this review, we discuss the potential utility of molecular analysis of the urine to provide a dynamic window into intrarenal molecular and morphologic responses. We focus on molecular analysis of the urine to identify noninvasive surrogate markers of kidney responses, with the goal of using these biomarkers as more sensitive indicators of progression and tissue-level responses to therapeutic interventions in patients with primary glomerulonephritis.
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Affiliation(s)
- Heather N Reich
- The Toronto Glomerulonephritis Registry, University Health Network, Gabor Zellerman Chair in Nephrology Research at the University of Toronto Department of Medicine, Toronto, Ontario, Canada.
| | - Veronica Y Sabelnykova
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Paul C Boutros
- Informatics and Bio-computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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21
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Pontillo C, Filip S, Borràs DM, Mullen W, Vlahou A, Mischak H. CE-MS-based proteomics in biomarker discovery and clinical application. Proteomics Clin Appl 2015; 9:322-34. [DOI: 10.1002/prca.201400115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/10/2014] [Accepted: 01/14/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Claudia Pontillo
- Department of R&D; Mosaiques Diagnostics GmbH; Hanover Germany
- Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Szymon Filip
- Charité-Universitätsmedizin Berlin; Berlin Germany
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
| | - Daniel M. Borràs
- Department of R&D; ServiceXS; Leiden The Netherlands
- Institut National de la Santé et de la Recherche Médicale (INSERM); Institute of Cardiovascular and Metabolic Disease; Toulouse France
- Université Toulouse III Paul-Sabatier; Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
| | - Antonia Vlahou
- Biotechnology Division; Biomedical Research Foundation; Academy of Athens; Athens Greece
- School of Biomedical and Healthcare Sciences; Plymouth University; Plymouth UK
| | - Harald Mischak
- Department of R&D; Mosaiques Diagnostics GmbH; Hanover Germany
- Institute of Cardiovascular and Medical Sciences; University of Glasgow; Glasgow UK
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22
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Abstract
Proteomic biomarkers offer the hope of improving the management of patients with kidney diseases by enabling more accurate and earlier detection of renal pathology than is possible with currently available biomarkers, serum creatinine and urinary albumin. In addition, proteomic biomarkers could also be useful to define the most suitable therapeutic targets in a given patient or disease setting. This Review describes the current status of proteomic and protein biomarkers in the context of kidney diseases. The valuable lessons learned from early clinical studies of potential proteomic biomarkers in kidney disease are presented to give context to the newly identified biomarkers, which have potential for actual clinical implementation. This article also includes an overview of protein-based biomarker candidates that are undergoing development for use in nephrology, focusing on those with the greatest potential for clinical implementation. Relevant issues and problems associated with the discovery, validation and clinical application of proteomic biomarkers are discussed, along with suggestions for solutions that might help to guide the design of future proteomic studies. These improvements might remove some of the current obstacles to the utilization of proteomic biomarkers, with potentially beneficial results.
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Hamilton P, Myers J, Gillham J, Ayers G, Brown N, Venning M. Urinary protein selectivity in nephrotic syndrome and pregnancy: resurrection of a biomarker when renal biopsy is contraindicated. Clin Kidney J 2014; 7:595-8. [PMID: 25859379 PMCID: PMC4389140 DOI: 10.1093/ckj/sfu103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 09/08/2014] [Indexed: 11/14/2022] Open
Abstract
Significant proteinuria in pregnancy can indicate the presence of serious conditions requiring investigation and treatment. The nephrotic syndrome in pregnancy presents a multitude of difficulties and is a relative contraindication of renal biopsy, particularly in the third trimester. We present a case of nephrotic syndrome of unknown cause presenting at 33 weeks of pregnancy. With renal biopsy contraindicated, we used the urine protein selectivity test, a largely discarded test predicting steroid-responsive nephrotic syndrome, to help inform the decision to give steroids. This led to a successful clinical outcome including the avoidance of neonatal ICU care for baby.
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Affiliation(s)
- Patrick Hamilton
- Manchester Institute of Nephrology & Transplantation, Manchester Royal Infirmary, Manchester, UK
| | - Jenny Myers
- Maternal & Fetal Health Research Centre, St Mary's Hospital, Manchester, UK
| | - Joanna Gillham
- Department of Obstetrics & Maternal and Fetal Medicine, St Mary's Hospital, Manchester, UK
| | - Gwen Ayers
- Department of Clinical Biochemistry, Manchester Royal Infirmary, Manchester, UK
| | - Nina Brown
- Manchester Institute of Nephrology & Transplantation, Manchester Royal Infirmary, Manchester, UK
| | - Michael Venning
- Manchester Institute of Nephrology & Transplantation, Manchester Royal Infirmary, Manchester, UK
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Urine Reflection of Changes in Blood. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 845:13-9. [DOI: 10.1007/978-94-017-9523-4_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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From hundreds to thousands: Widening the normal human Urinome (1). J Proteomics 2014; 112:53-62. [PMID: 25123350 DOI: 10.1016/j.jprot.2014.07.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/22/2022]
Abstract
UNLABELLED It is currently unknown how many proteins can be detected in urine. Improving the analytical approach would increase their number and potentially strengthen their predictive potential in diseases. We developed a combination of analytical procedures for maximizing sensitivity and reproducibility of normal human urinary proteome analysis based on ultracentrifugation, vesicles separation, combinatorial peptide ligand libraries (CPLL) and solvent removal of pigments. Proteins were identified by an Orbitrap Velos Mass Spectrometry. Overall, 3429 proteins were characterized: most components (1615) were contained in vesicles while the remaining 1794 were equally distributed among CPLL and butanol insoluble fractions. Several proteins were detected exclusively in one of the phases of the procedure, suggesting that each step is crucial in the fractionation strategy. Many (1724) proteins are described here whose presence in urine has never been reported and represents a potential source of information considering that urine is the unique site of excretion of products of interaction of metabolic processes. Improving the characterization of normal urinary proteome would also represent the basis for the analysis of urine biomarkers in human diseases. BIOLOGICAL SIGNIFICANCE Sub-fractionating normal urine by successive steps (vesicle separation, CPLL and solvent treatments) allowed the identification of 3429 proteins, a relevant part (1724) being detected for the first time in urine. Several proteins of new description have been implicated in physiology pathways and in pathologies thus representing a potential source of new information on both metabolic processes and diseases.
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Filip S, Pontillo C, Peter Schanstra J, Vlahou A, Mischak H, Klein J. Urinary proteomics and molecular determinants of chronic kidney disease: possible link to proteases. Expert Rev Proteomics 2014; 11:535-48. [DOI: 10.1586/14789450.2014.926224] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Changes of proteins induced by anticoagulants can be more sensitively detected in urine than in plasma. SCIENCE CHINA-LIFE SCIENCES 2014; 57:649-56. [PMID: 24907934 DOI: 10.1007/s11427-014-4661-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 03/14/2014] [Indexed: 01/06/2023]
Abstract
The most fundamental property of biomarkers is change. But changes are hard to maintain in plasma since it is strictly controlled by homeostatic mechanisms of the body. There is no homeostatic mechanism for urine. Besides, urine is partly a filtration of blood, and systematic information can be reflected in urine. We hypothesize that change of blood can be reflected in urine more sensitively. Here we introduce the interference into the blood by two anticoagulants heparin or argatroban. Plasma and urine proteins were profiled by LC-MS/MS and then validated by Western blot in totally six SD female rats before and after the drug treatments. In argatroban treated group, with exactly the same experimental procedure and the same cutoff value for both plasma and urine proteins, 62 proteins changed in urine, only one of which changed in plasma. In heparin treated group, 27 proteins changed in urine but only three other proteins changed in plasma. Both LC-MS/MS and Western blot analyses demonstrated drug-induced increases in transferrin and hemopexin levels in urine but not in plasma. Our data indicates that urine may serve as a source for more sensitive detection of protein biomarkers than plasma.
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Bakun M, Senatorski G, Rubel T, Lukasik A, Zielenkiewicz P, Dadlez M, Paczek L. Urine proteomes of healthy aging humans reveal extracellular matrix (ECM) alterations and immune system dysfunction. AGE (DORDRECHT, NETHERLANDS) 2014; 36:299-311. [PMID: 23917802 PMCID: PMC3889913 DOI: 10.1007/s11357-013-9562-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 07/01/2013] [Indexed: 05/02/2023]
Abstract
Aging is a complex physiological process that poses considerable conundrums to rapidly aging societies. For example, the risk of dying from cardiovascular diseases and/or cancer steadily declines for people after their 60s, and other causes of death predominate for seniors older than 80 years of age. Thus, physiological aging presents numerous unanswered questions, particularly with regard to changing metabolic patterns. Urine proteomics analysis is becoming a non-invasive and reproducible diagnostic method. We investigated the urine proteomes in healthy elderly people to determine which metabolic processes were weakened or strengthened in aging humans. Urine samples from 37 healthy volunteers aged 19-90 years (19 men, 18 women) were analyzed for protein expression by liquid chromatography-tandem mass spectrometry. This generated a list of 19 proteins that were differentially expressed in different age groups (young, intermediate, and old age). In particular, the oldest group showed protein changes reflective of altered extracellular matrix turnover and declining immune function, in which changes corresponded to reported changes in cardiovascular tissue remodeling and immune disorders in the elderly. Thus, urinary proteome changes in the elderly appear to reflect the physiological processes of aging and are particularly clearly represented in the circulatory and immune systems. Detailed identification of "protein trails" creates a more global picture of metabolic changes that occur in the elderly.
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Affiliation(s)
- M. Bakun
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland
| | - G. Senatorski
- Department of Immunology, Transplantology and Internal Diseases, Transplantation Institute, Medical University of Warsaw, ul. Nowogrodzka 59, 02-006 Warsaw, Poland
| | - T. Rubel
- Institute of Radioelectronics, Warsaw University of Technology, ul. Nowowiejska 15/19, 00-665 Warsaw, Poland
| | - A. Lukasik
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland
| | - P. Zielenkiewicz
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland
| | - M. Dadlez
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland
- Department of Biology, Warsaw University, ul. Miecznikowa 1, 02-096 Warsaw, Poland
| | - L. Paczek
- Department of Immunology, Transplantology and Internal Diseases, Transplantation Institute, Medical University of Warsaw, ul. Nowogrodzka 59, 02-006 Warsaw, Poland
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Findeisen P, Peccerella T, Neumaier M, Schadendorf D. Proteomics for biomarker discovery in malignant melanoma. ACTA ACUST UNITED AC 2014. [DOI: 10.1586/17469872.3.2.209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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30
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Thongboonkerd V. Proteomic analysis of renal diseases: unraveling the pathophysiology and biomarker discovery. Expert Rev Proteomics 2014; 2:349-66. [PMID: 16000082 DOI: 10.1586/14789450.2.3.349] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Current biomedical applications of proteomics have been conducted with four main objectives: to better understand the normal biology and physiology of cells, microorganisms, tissues and organs; to explore the pathogenic mechanisms and better understand the pathophysiology of medical diseases; to identify novel biomarkers for early disease detection, prediction and prognosis; and to define new therapeutic targets, drugs and vaccines. This review focuses predominantly on proteomic applications to unravel the pathophysiology and to define novel biomarkers for various renal diseases (i.e., glomerular diseases, tubulointerstitial diseases, renal vascular disorders and renal cancers). In addition, proteomic evaluations of renal transplantation and renal replacement therapy (for acute renal failure and end-stage renal disease) are summarized. Personal opinion, future perspectives and information resources for the field of renal and urinary proteomics are provided.
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Affiliation(s)
- Visith Thongboonkerd
- Siriraj Proteomics Center, Medical Molecular Biology Unit, Office for Research & Development, 12th Floor Adulyadej Vikrom Bldg, Siriraj Hospital, 2 Prannok Road, Bangkoknoi, Bangkok 10700, Thailand.
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31
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Albalat A, Mischak H, Mullen W. Clinical application of urinary proteomics/peptidomics. Expert Rev Proteomics 2014; 8:615-29. [DOI: 10.1586/epr.11.46] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Traum AZ. Urine proteomic profiling to identify biomarkers of steroid resistance in pediatric nephrotic syndrome. Expert Rev Proteomics 2014; 5:715-9. [DOI: 10.1586/14789450.5.5.715] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Isobe K, Mori T, Asano T, Kawaguchi H, Nonoyama S, Kumagai N, Kamada F, Morimoto T, Hayashi M, Sohara E, Rai T, Sasaki S, Uchida S. Development of enzyme-linked immunosorbent assays for urinary thiazide-sensitive Na-Cl cotransporter measurement. Am J Physiol Renal Physiol 2013; 305:F1374-81. [PMID: 24026181 DOI: 10.1152/ajprenal.00208.2013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The Na-Cl cotransporter (NCC) in the distal convoluted tubules in kidney is known to be excreted in urine. However, its clinical significance has not been established because of the lack of quantitative data on urinary NCC. We developed highly sensitive enzyme-linked immunosorbent assays (ELISAs) for urinary total NCC (tNCC) and its active form, phosphorylated NCC (pNCC). We first measured the excretion of tNCC and pT55-NCC in urinary exosomes in pseudohypoaldosteronism type II (PHAII) patients since PHAII is caused by NCC activation. Highly increased excretion of tNCC and pNCC was observed in PHAII patients. In contrast, the levels of tNCC and pNCC in the urine of patients with Gitelman's syndrome were not detectable or very low, indicating that both assays could specifically detect the changes in urinary NCC excretion caused by the changes of NCC activity in the kidney. Then, to test whether these assays could be feasible for a more general patient population, we measured tNCC and pNCC in the urine of outpatients with different clinical backgrounds. Although urinary protein levels >30 mg/dl interfered with our ELISA, we could measure urinary pNCC in all patients without proteinuria. Thus we established highly sensitive and quantitative assays for urinary NCC, which could be valuable tools for estimating NCC activity in vivo.
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Affiliation(s)
- Kiyoshi Isobe
- Dept. of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental Univ., 1-5-45 Yushima, Bunkyo, Tokyo 113-8519, Japan.
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Neuhaus J, Schiffer E, von Wilcke P, Bauer HW, Leung H, Siwy J, Ulrici W, Paasch U, Horn LC, Stolzenburg JU. Seminal plasma as a source of prostate cancer peptide biomarker candidates for detection of indolent and advanced disease. PLoS One 2013; 8:e67514. [PMID: 23826311 PMCID: PMC3691205 DOI: 10.1371/journal.pone.0067514] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 05/23/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Extensive prostate specific antigen screening for prostate cancer generates a high number of unnecessary biopsies and over-treatment due to insufficient differentiation between indolent and aggressive tumours. We hypothesized that seminal plasma is a robust source of novel prostate cancer (PCa) biomarkers with the potential to improve primary diagnosis of and to distinguish advanced from indolent disease. METHODOLOGY/PRINCIPAL FINDINGS In an open-label case/control study 125 patients (70 PCa, 21 benign prostate hyperplasia, 25 chronic prostatitis, 9 healthy controls) were enrolled in 3 centres. Biomarker panels a) for PCa diagnosis (comparison of PCa patients versus benign controls) and b) for advanced disease (comparison of patients with post surgery Gleason score <7 versus Gleason score >7) were sought. Independent cohorts were used for proteomic biomarker discovery and testing the performance of the identified biomarker profiles. Seminal plasma was profiled using capillary electrophoresis mass spectrometry. Pre-analytical stability and analytical precision of the proteome analysis were determined. Support vector machine learning was used for classification. Stepwise application of two biomarker signatures with 21 and 5 biomarkers provided 83% sensitivity and 67% specificity for PCa detection in a test set of samples. A panel of 11 biomarkers for advanced disease discriminated between patients with Gleason score 7 and organ-confined (<pT3a) or advanced (≥pT3a) disease with 80% sensitivity and 82% specificity in a preliminary validation setting. Seminal profiles showed excellent pre-analytical stability. Eight biomarkers were identified as fragments of N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase, prostatic acid phosphatase, stabilin-2, GTPase IMAP family member 6, semenogelin-1 and -2. Restricted sample size was the major limitation of the study. CONCLUSIONS/SIGNIFICANCE Seminal plasma represents a robust source of potential peptide makers for primary PCa diagnosis. Our findings warrant further prospective validation to confirm the diagnostic potential of identified seminal biomarker candidates.
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Affiliation(s)
- Jochen Neuhaus
- University of Leipzig, Department of Urology, Leipzig, Germany.
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Li B, Petersen NJ, Andersen LH, Hansen SH. Easy peak tracking in CE-UV and CE-UV-ESI-MS by incorporating temperature-correlated mobility scaling. Electrophoresis 2013; 34:1787-95. [DOI: 10.1002/elps.201200695] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/04/2013] [Accepted: 03/25/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Bin Li
- Department of Pharmacy, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen; Denmark
| | - Nickolaj J. Petersen
- Department of Pharmacy, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen; Denmark
| | - Line H. Andersen
- Department of Pharmacy, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen; Denmark
| | - Steen H. Hansen
- Department of Pharmacy, Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen; Denmark
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Zürbig P, Jahn H. Use of proteomic methods in the analysis of human body fluids in Alzheimer research. Electrophoresis 2013; 33:3617-30. [PMID: 23160951 DOI: 10.1002/elps.201200360] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/27/2012] [Accepted: 09/27/2012] [Indexed: 01/23/2023]
Abstract
Proteomics is the study of the entire population of proteins and peptides in an organism or a part of it, such as a cell, tissue, or fluids like cerebrospinal fluid, plasma, serum, urine, or saliva. It is widely assumed that changes in the composition of the proteome may reflect disease states and provide clues to its origin, eventually leading to targets for new treatments. The ability to perform large-scale proteomic studies now is based jointly on recent advances in our analytical methods. Separation techniques like CE and 2DE have developed and matured. Detection methods like MS have also improved greatly in the last 5 years. These developments have also driven the fields of bioinformatics, needed to deal with the increased data production and systems biology. All these developing methods offer specific advantages but also come with certain limitations. This review describes the different proteomic methods used in the field, their limitations, and their possible pitfalls. Based on a literature search in PubMed, we identified 112 studies that applied proteomic techniques to identify biomarkers for Alzheimer disease. This review describes the results of these studies on proteome changes in human body fluids of Alzheimer patients reviewing the most important studies. We extracted a list of 366 proteins and peptides that were identified by these studies as potential targets in Alzheimer research.
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Graterol F, Navarro-Muñoz M, Ibernon M, López D, Troya MI, Pérez V, Bonet J, Romero R. Poor histological lesions in IgA nephropathy may be reflected in blood and urine peptide profiling. BMC Nephrol 2013; 14:82. [PMID: 23577616 PMCID: PMC3637490 DOI: 10.1186/1471-2369-14-82] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 04/05/2013] [Indexed: 01/01/2023] Open
Abstract
Background IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide, leading to renal failure in 15% to 40% of cases. IgAN is diagnosed by renal biopsy, an invasive method that is not risk-free. We used blood and urine peptide profiles as a noninvasive method of linking IgAN-associated changes with histological lesions by Oxford classification. Methods We prospectively studied 19 patients with biopsy-proven IgAN and 14 healthy subjects from 2006 to 2009, excluding subjects with crescentic glomerulonephritis and collecting clinical and biochemical data at the time of diagnosis and during follow-up (24 months). Histological lesions were evaluated by Oxford classification. Proteomic analysis was performed by combining magnetic bead (MB) technology and mass spectrometry (MALDI-TOF MS) to obtain peptide profiles. Doubling of serum creatinine was considered a variable of poor renal prognosis. Results We identified 55 peptides—13 in serum, 26 in plasma, and 16 in urine—that differentiated IgAN patients from healthy subjects. A significant association was noted between serum/plasma and urine peptides and histological findings—ie, tubulointerstitial damage, segmental glomerulosclerosis, and endocapillary injury. We also identified 3 peptides—corresponding to bradykinin, uromodulin, and alpha-1-antitrypsin—that were associated with severity of lesions, such as tubulointerstitial damage and segmental glomerulosclerosis. Moreover, blood peptides with m/z 2953, 5337, 9287, and 9289 and urine peptides with m/z 1769, 1898, 1913, 1945, 2491, 2756, 2977, 3004, 3389, and 4752 correlated significantly with poor renal function. Conclusions In patients with IgAN, the use of noninvasive approaches, such as blood and urine proteomics, can provide valuable information beyond that of standard diagnostic techniques, allowing us to identify blood and urine peptide profiles that are associated with poor histological lesions in IgAN patients.
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Wood SL, Knowles MA, Thompson D, Selby PJ, Banks RE. Proteomic studies of urinary biomarkers for prostate, bladder and kidney cancers. Nat Rev Urol 2013; 10:206-18. [PMID: 23443013 DOI: 10.1038/nrurol.2013.24] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Urine is an ideal body fluid for the detection of protein markers produced by urological cancers as it can be sampled noninvasively and contains secreted and directly shed proteins from the prostate, bladder and kidney. Major challenges of working with urine include high inter-individual and intra-individual variability, low protein concentration, the presence of salts and the dynamic range of protein expression. Despite these challenges, significant progress is being made using modern proteomic methods to identify and characterize protein-based markers for urological cancers. The development of robust, easy-to-use clinical tests based on novel biomarkers has the potential to impact upon diagnosis, prognosis and monitoring and could revolutionize the treatment and management of these cancers.
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Affiliation(s)
- Steven L Wood
- Wolfson Molecular Imaging Centre, 27 Palatine Road, Withington, Manchester M20 3LJ, UK.
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Albalat A, Bitsika V, Zurbig P, Siwy J, Mullen W. High-resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Methods Mol Biol 2013; 984:153-165. [PMID: 23386343 DOI: 10.1007/978-1-62703-296-4_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The analysis of proteins and peptides in biological fluids is becoming more important as they are potential sources of diagnostic biomarkers of disease. The complexity of body fluids is such that no single technique can both identify and quantify all the constituents present. It therefore requires pre-concentration of the compounds of interest and hyphenated techniques like capillary electrophoresis (CE) or high-performance liquid chromatography (HPLC) coupled to a mass spectrometer (MS) to provide the separation, identification, and quantification of the proteins and peptides under investigation. Here we provide protocols for sample preparation of various body fluids, namely, urine, plasma, and cerebrospinal fluid, and how to obtain maximum sensitivity and selectivity of the small proteins and peptides under investigation by CE-MS.
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Affiliation(s)
- Amaya Albalat
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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A comparison between MALDI-MS and CE-MS data for biomarker assessment in chronic kidney diseases. J Proteomics 2012; 75:5888-97. [DOI: 10.1016/j.jprot.2012.07.024] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 06/25/2012] [Accepted: 07/16/2012] [Indexed: 11/22/2022]
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Huang Z, Hong Q, Xue P, Paul G, Feng Z, Wang L, Mei Y, Wu L, Chen X, Wu D. A proteome-wide screen identifies valosin-containing protein as an essential regulator of podocyte endoplasmic reticulum stress. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5250-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Xu Q, Cui Z, Venkatraman G, Gomes AV. The use of biophysical proteomic techniques in advancing our understanding of diseases. Biophys Rev 2012; 4:125-135. [PMID: 28510094 PMCID: PMC5418381 DOI: 10.1007/s12551-012-0070-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 01/26/2012] [Indexed: 12/14/2022] Open
Abstract
The use of proteomic approaches in investigating diseases is continuing to expand and has started to provide answers to substantial gaps in our understanding of disease pathogenesis as well as in the development of effective strategies for the early diagnosis and treatment of diseases. Biophysical techniques form a crucial part of the advanced proteomic techniques currently used and include mass spectrometry and protein separation techniques, such as two-dimensional gel electrophoresis and liquid chromatography. The application of biophysical proteomic techniques in the study of disease includes delineation of altered protein expression, not only at the whole-cell or tissue levels, but also in subcellular structures, protein complexes, and biological fluids. These techniques are also being used for the discovery of novel disease biomarkers, exploration of the pathogenesis of diseases, development of new diagnostic methodologies, and identification of new targets for therapeutics. Proteomic techniques also have the potential for accelerating drug development through more effective strategies for evaluating a specific drug's therapeutic effects and toxicity. This article discusses the application of biophysical proteomic techniques in delineating cardiovascular disease and other diseases, as well as the limitations and future research directions required for these techniques to gain greater acceptance and have a larger impact.
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Affiliation(s)
- Qian Xu
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Ziyou Cui
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Gayathi Venkatraman
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA
| | - Aldrin V Gomes
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, 176 Briggs Hall, One Shields Avenue, Davis, CA, 95616, USA.
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Rouse R, Siwy J, Mullen W, Mischak H, Metzger J, Hanig J. Proteomic candidate biomarkers of drug-induced nephrotoxicity in the rat. PLoS One 2012; 7:e34606. [PMID: 22509332 PMCID: PMC3324487 DOI: 10.1371/journal.pone.0034606] [Citation(s) in RCA: 21] [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: 10/19/2011] [Accepted: 03/05/2012] [Indexed: 01/14/2023] Open
Abstract
Improved biomarkers of acute nephrotoxicity are coveted by the drug development industry, regulatory agencies, and clinicians. In an effort to identify such biomarkers, urinary peptide profiles of rats treated with two different nephrotoxins were investigated. 493 marker candidates were defined that showed a significant response to cis-platin comparing a cis-platin treated cohort to controls. Next, urine samples from rats that received three consecutive daily doses of 150 or 300 mg/kg gentamicin were examined. 557 potential biomarkers were initially identified; 108 of these gentamicin-response markers showed a clear temporal response to treatment. 39 of the cisplatin-response markers also displayed a clear response to gentamicin. Of the combined 147 peptides, 101 were similarly regulated by gentamicin or cis-platin and 54 could be identified by tandem mass spectrometry. Most were collagen type I and type III fragments up-regulated in response to gentamicin treatment. Based on these peptides, classification models were generated and validated in a longitudinal study. In agreement with histopathology, the observed changes in classification scores were transient, initiated after the first dose, and generally persistent over a period of 10–20 days before returning to control levels. The data support the hypothesis that gentamicin-induced renal toxicity up-regulates protease activity, resulting in an increase in several specific urinary collagen fragments. Urinary proteomic biomarkers identified here, especially those common to both nephrotoxins, may serve as a valuable tool to investigate potential new drug candidates for the risk of nephrotoxicity.
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Affiliation(s)
- Rodney Rouse
- Division of Drug Safety Research, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, Maryland, United States of America.
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Valganciclovir prophylaxis versus preemptive therapy in cytomegalovirus-positive renal allograft recipients: 1-year results of a randomized clinical trial. Transplantation 2012; 93:61-8. [PMID: 22094954 DOI: 10.1097/tp.0b013e318238dab3] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Cytomegalovirus (CMV) prevention can be achieved by prophylaxis or preemptive therapy. We performed a prospective randomized trial to determine whether renal transplant recipients with a positive CMV serostatus (R+) had a higher rate of CMV infection and disease after transplantation when treated preemptively for CMV infection, compared with primary valganciclovir prophylaxis. METHODS Prophylaxis was 2 × 450 mg oral valganciclovir/day for 100 days; preemptive patients were monitored by CMV-polymerase chain reaction (PCR), and after a positive PCR test received 2 × 900 mg valganciclovir/day for at least 14 days followed by secondary prophylaxis. Valganciclovir dosage was adjusted according to renal function. Patients are followed up for 5 years and initial 12-month data are presented. Two hundred and ninety-six recipients were analyzed (168 donor/recipient seropositive [D+/R+], 128 donor seronegative/recipient seropositive [D-/R+]; 146 receiving prophylaxis and 150 preemptive therapy). RESULTS Overall, CMV infection (asymptomatic CMV viral load ≥ 400 CMV DNA copies/mL proven by CMV-PCR) was significantly higher in recipients under preemptive therapy (38.7% vs. 11.0%, P<0.0001), with the highest incidence in D+/R+ preemptive patients (53.8% vs. 15.6%, P<0.0001). D+/R+ recipients with preemptive therapy also had the highest rate of CMV disease (CMV syndrome and tissue-invasive disease that was clinically diagnosed and biopsy proven) (19.2% vs. 4.4%, P=0.003). Renal function assessed by creatinine clearance was similar for both groups. Graft loss occurred in 7 vs. 4 patients on preemptive versus prophylactic therapy (P>0.05). Tolerability was similar for both treatment groups. CONCLUSIONS Oral valganciclovir prophylaxis significantly reduces CMV infection and disease, particularly for D+/R+ patients. Hence, our study supports routine prophylaxis for all D+/R+ recipients.
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Navarro-Muñoz M, Ibernon M, Bonet J, Pérez V, Pastor MC, Bayés B, Casado-Vela J, Navarro M, Ara J, Espinal A, Fluvià L, Serra A, López D, Romero R. Uromodulin and α(1)-antitrypsin urinary peptide analysis to differentiate glomerular kidney diseases. Kidney Blood Press Res 2012; 35:314-25. [PMID: 22399069 DOI: 10.1159/000335383] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 11/23/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Glomerular kidney disease (GKD) is suspected in patients based on proteinuria, but its diagnosis relies primarily on renal biopsy. We used urine peptide profiling as a noninvasive means to link GKD-associated changes to each glomerular entity. METHODS Urinary peptide profiles of 60 biopsy-proven glomerular patients and 14 controls were analyzed by combining magnetic bead peptide enrichment, MALDI-TOF MS analysis, and ClinProTools v2.0 to select differential peptides. Tentative identification of the differential peptides was carried out by HPLC-MS/MS. RESULTS The HPLC-MS/MS results suggest that uromodulin (UMOD; m/z: 1682, 1898 and 1913) and α(1)-antitrypsin (A1AT; m/z: 1945, 2392 and 2505) are differentially expressed urinary peptides that distinguish between GKD patients and healthy subjects. Low UMOD and high A1AT peptide abundance was observed in 80-92% of patients with GKD. Proliferative forms of GKD were distinguished from nonproliferative forms, based on a combination of UMOD and A1AT peptides. Nonproliferative forms correlated with higher A1AT peptide levels - focal segmental glomerulosclerosis was linked more closely to high levels of the m/z 1945 peptide than minimal change disease. CONCLUSION We describe a workflow - urinary peptide profiling coupled with histological findings - that can be used to distinguish GKD accurately and noninvasively, particularly its nonproliferative forms.
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Affiliation(s)
- Maribel Navarro-Muñoz
- Department of Nephrology, Germans Trias i Pujol Hospital, Autonomous University of Barcelona, Esfera UAB, Badalona, Spain
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von zur Muhlen C, Schiffer E, Sackmann C, Zürbig P, Neudorfer I, Zirlik A, Htun N, Iphöfer A, Jänsch L, Mischak H, Bode C, Chen YC, Peter K. Urine proteome analysis reflects atherosclerotic disease in an ApoE-/- mouse model and allows the discovery of new candidate biomarkers in mouse and human atherosclerosis. Mol Cell Proteomics 2012; 11:M111.013847. [PMID: 22371488 DOI: 10.1074/mcp.m111.013847] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Noninvasive diagnosis of atherosclerosis via single biomarkers has been attempted but remains elusive. However, a previous polymarker or pattern approach of urine polypeptides in humans reflected coronary artery disease with high accuracy. The aim of the current study is to use urine proteomics in ApoE(-/-) mice to discover proteins with pathophysiological roles in atherogenesis and to identify urinary polypeptide patterns reflecting early stages of atherosclerosis. Urine of ApoE(-/-) mice either on high fat diet (HFD) or chow diet was collected over 12 weeks; urine of wild type mice on HFD was used to exclude diet-related proteome changes. Capillary electrophoresis coupled to mass spectrometry (CE-MS) of samples identified 16 polypeptides specific for ApoE(-/-) mice on HFD. In a blinded test set, these polypeptides allowed identification of atherosclerosis at a sensitivity of 90% and specificity of 100%, as well as monitoring of disease progression. Sequencing of the discovered polypeptides identified fragments of α(1)-antitrypsin, epidermal growth factor (EGF), kidney androgen-regulated protein, and collagen. Using immunohistochemistry, α(1)-antitrypsin, EGF, and collagen type I were shown to be highly expressed in atherosclerotic plaques of ApoE(-/-) mice on HFD. Urinary excretion levels of collagen and α(1)-antitrypsin fragments also significantly correlated with intraplaque collagen and α(1)-antitrypsin content, mirroring plaque protein expression in the urine proteome. To provide further confirmation that the newly identified proteins are relevant in humans, the presence of collagen type I, α(1)-antitrypsin, and EGF was also confirmed in human atherosclerotic disease. Urine proteome analysis in mice exemplifies the potential of a novel multimarker approach for the noninvasive detection of atherosclerosis and monitoring of disease progression. Furthermore, this approach represents a novel discovery tool for the identification of proteins relevant in murine and human atherosclerosis and thus also defines potential novel therapeutic targets.
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Drube J, Schiffer E, Lau E, Petersen C, Kirschstein M, Kemper MJ, Lichtinghagen R, Ure B, Mischak H, Pape L, Ehrich JHH. Urinary proteome analysis to exclude severe vesicoureteral reflux. Pediatrics 2012; 129:e356-63. [PMID: 22271698 DOI: 10.1542/peds.2010-3467] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES High-grade vesicoureteral reflux (VUR, grade IV or V) is a risk factor for renal scarring, impaired renal function, and arterial hypertension. Voiding cystourethrography is the gold standard for detecting the severity of VUR. High-grade VUR is present in the minority of children with urinary tract infection (UTI), thus exposing the majority to invasive diagnostics that have no surgical consequence. We therefore aimed at establishing a noninvasive test to identify children with high-grade VUR. METHODS In a case-control study, a specific urinary proteome pattern was established by capillary electrophoresis coupled to mass spectrometry in 18 patients with primary VUR grade IV or V, distinguishing these from 19 patients without VUR after UTI. This proteome pattern was independently validated in a blinded cohort of 17 patients with VUR grade IV or V and 19 patients without VUR. RESULTS Sensitivity in detecting VUR grade IV or V in the blinded study was 88%, specificity was 79%. The test's accuracy was independent of age, gender, and grade of VUR in the contralateral kidney. The odds ratio of suffering from VUR grade IV or V when tested positive was 28 (95% confidence interval: 4.5 to 176.0). CONCLUSIONS This noninvasive test is ready for prospective validation in large cohorts with the aim of identifying those children with UTI and hydronephrosis in need of further invasive diagnostics, such as voiding cystourethrography, thus sparing most children without pathologic urinary proteome patterns from additional diagnostics.
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Affiliation(s)
- Jens Drube
- Clinic of Pediatric Kidney, Liver and Metabolic Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
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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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Jahn H, Wittke S, Zürbig P, Raedler TJ, Arlt S, Kellmann M, Mullen W, Eichenlaub M, Mischak H, Wiedemann K. Peptide fingerprinting of Alzheimer's disease in cerebrospinal fluid: identification and prospective evaluation of new synaptic biomarkers. PLoS One 2011; 6:e26540. [PMID: 22046305 PMCID: PMC3202544 DOI: 10.1371/journal.pone.0026540] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 09/28/2011] [Indexed: 12/03/2022] Open
Abstract
Background Today, dementias are diagnosed late in the course of disease. Future treatments have to start earlier in the disease process to avoid disability requiring new diagnostic tools. The objective of this study is to develop a new method for the differential diagnosis and identification of new biomarkers of Alzheimer's disease (AD) using capillary-electrophoresis coupled to mass-spectrometry (CE-MS) and to assess the potential of early diagnosis of AD. Methods and Findings Cerebrospinal fluid (CSF) of 159 out-patients of a memory-clinic at a University Hospital suffering from neurodegenerative disorders and 17 cognitively-healthy controls was used to create differential peptide pattern for dementias and prospective blinded-comparison of sensitivity and specificity for AD diagnosis against the Criterion standard in a naturalistic prospective sample of patients. Sensitivity and specificity of the new method compared to standard diagnostic procedures and identification of new putative biomarkers for AD was the main outcome measure. CE-MS was used to reliably detect 1104 low-molecular-weight peptides in CSF. Training-sets of patients with clinically secured sporadic Alzheimer's disease, frontotemporal dementia, and cognitively healthy controls allowed establishing discriminative biomarker pattern for diagnosis of AD. This pattern was already detectable in patients with mild cognitive impairment (MCI). The AD-pattern was tested in a prospective sample of patients (n = 100) and AD was diagnosed with a sensitivity of 87% and a specificity of 83%. Using CSF measurements of beta-amyloid1-42, total-tau, and phospho181-tau, AD-diagnosis had a sensitivity of 88% and a specificity of 67% in the same sample. Sequence analysis of the discriminating biomarkers identified fragments of synaptic proteins like proSAAS, apolipoprotein J, neurosecretory protein VGF, phospholemman, and chromogranin A. Conclusions The method may allow early differential diagnosis of various dementias using specific peptide fingerprints and identification of incipient AD in patients suffering from MCI. Identified biomarkers facilitate face validity for the use in AD diagnosis.
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Affiliation(s)
- Holger Jahn
- Department of Psychiatry, University Hospital Hamburg-Eppendorf, Hamburg, Germany.
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Markers of vascular disease in plasma from patients with chronic kidney disease identified by proteomic analysis. J Hypertens 2011; 29:783-90. [DOI: 10.1097/hjh.0b013e3283441129] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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