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Mischak H, Kalvodova L. Interview with Harald Mischak. Proteomics 2022; 22:e2100390. [PMID: 35112791 DOI: 10.1002/pmic.202100390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/11/2022]
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2
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He T, Pejchinovski M, Mullen W, Beige J, Mischak H, Jankowski V. Peptides in Plasma, Urine, and Dialysate: Toward Unravelling Renal Peptide Handling. Proteomics Clin Appl 2020; 15:e2000029. [PMID: 32618437 DOI: 10.1002/prca.202000029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/11/2020] [Indexed: 12/28/2022]
Abstract
PURPOSE The peptidomes of spent hemodialysate, urine, and plasma are investigated, to shed light on peptide handling in the kidney. EXPERIMENTAL DESIGN Fifteen plasma, 15 urine, and 13 spent hemodialysate samples are collected from age- and sex-matched subjects with chronic kidney disease. Peptide identification and quantification are performed with capillary electrophoresis-coupled mass spectrometry. RESULTS A total of 6278 urinary peptides, 1743 plasma peptides, and 1727 peptides from spent hemodialysate are detected. Of these, sequences can be assigned to 1580, 419, and 352 peptides, respectively. A strong correlation in peptide abundance between urine and spent hemodialysate (p = 3 × 10-21 , Rho = 0.52), a moderately strong correlation between spent hemodialysate and plasma (p = 4.5 × 10-5 , Rho = 0.30), and no significant correlation between urine and plasma (p = 0.11, Rho = 0.094) are found. Collagen and fibrinogen alpha peptides are highly abundant in all three body fluids. In spent hemodialysate, thymosin ß4 is one of the most abundant peptides, which is shown to be negatively associated with the estimated glomerular filtration rate (Rho = -0.39, p-value = 3.9 × 10-81 ). CONCLUSION AND CLINICAL RELEVANCE The correlation of peptide abundance in these three body fluids is lower than expected, supporting the hypothesis that tubular reabsorption has a major impact on urinary peptide content. Further investigation of thymosin ß4 in hemodialysis is thus warranted.
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Affiliation(s)
- Tianlin He
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute for Molecular Cardiovascular Research (IMCAR), University of Aachen, Aachen, Germany
| | | | - William Mullen
- Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, UK
| | - Joachim Beige
- Department of Nephrology and Kuratorium for Dialysis and Transplantation (KfH) Renal Unit, Hospital St. Georg, Leipzig, Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany.,Institute of Cardiovascular and Medical Science, University of Glasgow, Glasgow, UK
| | - Vera Jankowski
- Institute for Molecular Cardiovascular Research (IMCAR), University of Aachen, Aachen, Germany
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3
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Wang D, Yang J, Fan J, Chen W, Nikolic‐Paterson DJ, Li J. Omics technologies for kidney disease research. Anat Rec (Hoboken) 2020; 303:2729-2742. [PMID: 32592293 DOI: 10.1002/ar.24413] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/31/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jiayi Yang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Jinjin Fan
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
| | | | - Jinhua Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen University Guangzhou China
- Key Laboratory of Nephrology, National Health Commission and Guangdong Province Guangzhou China
- Shunde Women and Children Hospital, Guangdong Medical University Shunde Guangdong China
- The Second Clinical College, Guangdong Medical University Dongguan Guangdong China
- Department of Anatomy and Developmental BiologyMonash Biomedicine Discovery Institute, Monash University Clayton Victoria Australia
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4
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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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Abstract
Proteome analysis has been applied in multiple studies in the context of chronic kidney disease, aiming at improving our knowledge on the molecular pathophysiology of the disease. The approach is generally based on the hypothesis that proteins are key in maintaining kidney function, and disease is a clinical consequence of a significant change of the protein level. Knowledge on critical proteins and their alteration in disease should in turn enable identification of ideal biomarkers that could guide patient management. In addition, all drugs currently employed target proteins. Hence, proteome analysis also promises to enable identifying the best suited therapeutic target, and, in combination with biomarkers, could be used as the rationale basis for personalized intervention. To assess the current status of proteome analysis in the context of CKD, we present the results of a systematic review, of up-to-date scientific research, and give an outlook on the developments that can be expected in near future. Based on the current literature, proteome analysis has already seen implementation in the management of CKD patients, and it is expected that this approach, also supported by the positive results generated to date, will see advanced high-throughput application.
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6
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CE-MS-based urinary biomarkers to distinguish non-significant from significant prostate cancer. Br J Cancer 2019; 120:1120-1128. [PMID: 31092909 PMCID: PMC6738044 DOI: 10.1038/s41416-019-0472-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 04/11/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
Background Prostate cancer progresses slowly when present in low risk forms but can be lethal when it progresses to metastatic disease. A non-invasive test that can detect significant prostate cancer is needed to guide patient management. Methods Capillary electrophoresis/mass spectrometry has been employed to identify urinary peptides that may accurately detect significant prostate cancer. Urine samples from 823 patients with PSA (<15 ng/ml) were collected prior to biopsy. A case–control comparison was performed in a training set of 543 patients (nSig = 98; nnon-Sig = 445) and a validation set of 280 patients (nSig = 48, nnon-Sig = 232). Totally, 19 significant peptides were subsequently combined by a support vector machine algorithm. Results Independent validation of the 19-biomarker model in 280 patients resulted in a 90% sensitivity and 59% specificity, with an AUC of 0.81, outperforming PSA (AUC = 0.58) and the ERSPC-3/4 risk calculator (AUC = 0.69) in the validation set. Conclusions This multi-parametric model holds promise to improve the current diagnosis of significant prostate cancer. This test as a guide to biopsy could help to decrease the number of biopsies and guide intervention. Nevertheless, further prospective validation in an external clinical cohort is required to assess the exact performance characteristics.
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7
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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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Ricci P, Magalhães P, Krochmal M, Pejchinovski M, Daina E, Caruso MR, Goea L, Belczacka I, Remuzzi G, Umbhauer M, Drube J, Pape L, Mischak H, Decramer S, Schaefer F, Schanstra JP, Cereghini S, Zürbig P. Urinary proteome signature of Renal Cysts and Diabetes syndrome in children. Sci Rep 2019; 9:2225. [PMID: 30778115 PMCID: PMC6379363 DOI: 10.1038/s41598-019-38713-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/17/2018] [Indexed: 12/27/2022] Open
Abstract
Renal Cysts and Diabetes Syndrome (RCAD) is an autosomal dominant disorder caused by mutations in the HNF1B gene encoding for the transcriptional factor hepatocyte nuclear factor-1B. RCAD is characterized as a multi-organ disease, with a broad spectrum of symptoms including kidney abnormalities (renal cysts, renal hypodysplasia, single kidney, horseshoe kidneys, hydronephrosis), early-onset diabetes mellitus, abnormal liver function, pancreatic hypoplasia and genital tract malformations. In the present study, using capillary electrophoresis coupled to mass spectrometry (CE-MS), we investigated the urinary proteome of a pediatric cohort of RCAD patients and different controls to identify peptide biomarkers and obtain further insights into the pathophysiology of this disorder. As a result, 146 peptides were found to be associated with RCAD in 22 pediatric patients when compared to 22 healthy age-matched controls. A classifier based on these peptides was generated and further tested on an independent cohort, clearly discriminating RCAD patients from different groups of controls. This study demonstrates that the urinary proteome of pediatric RCAD patients differs from autosomal dominant polycystic kidney disease (PKD1, PKD2), congenital nephrotic syndrome (NPHS1, NPHS2, NPHS4, NPHS9) as well as from chronic kidney disease conditions, suggesting differences between the pathophysiology behind these disorders.
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Affiliation(s)
- Pierbruno Ricci
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Pedro Magalhães
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | | | - Erica Daina
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri - Clinical Research Center for Rare Diseases Aldo e Cele Daccò, Ranica Bergamo, Italy
| | | | - Laura Goea
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Iwona Belczacka
- Mosaiques Diagnostics GmbH, Hannover, Germany
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), Aachen, Germany
| | - Giuseppe Remuzzi
- IRCCS - Istituto di Ricerche Farmacologiche Mario Negri - Clinical Research Center for Rare Diseases Aldo e Cele Daccò, Ranica Bergamo, Italy
| | - Muriel Umbhauer
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Jens Drube
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | - Lars Pape
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Stéphane Decramer
- Service de Néphrologie Pédiatrique, Hôpital des Enfants, CHU Toulouse, Toulouse, France
- Centre De Référence des Maladies Rénales Rares du Sud Ouest (SORARE), Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Franz Schaefer
- University Children Hospital, Pediatric Nephrology, Heidelberg, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Silvia Cereghini
- Sorbonne Université - CNRS - UMR7622 - Institut de Biologie Paris Seine (IBPS), Paris, France
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Siwy J, Klein T, Rosler M, von Eynatten M. Urinary Proteomics as a Tool to Identify Kidney Responders to Dipeptidyl Peptidase-4 Inhibition: A Hypothesis-Generating Analysis from the MARLINA-T2D Trial. Proteomics Clin Appl 2019; 13:e1800144. [PMID: 30632692 DOI: 10.1002/prca.201800144] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/27/2018] [Indexed: 01/13/2023]
Abstract
PURPOSE Chronic kidney disease (CKD) is a serious complication of hyperglycemia and treatment options to slow its progression are scarce. Dipeptidyl peptidase-4 (DPP-4) inhibitors are common glucose-lowering drugs in type 2 diabetes (T2D). Among these, linagliptin has been suggested to exert kidney protective effects. It is investigated whether an effect of linagliptin on kidney function could be unmasked by characterizing the urinary proteome profile (UPP) in albuminuric T2D individuals. EXPERIMENTAL DESIGN Participants of the MARLINA-T2D trial (NCT01792518) are randomized 1:1 to receive either linagliptin 5 mg or placebo for 24 weeks. A previously developed proteome-based classifier, CKD273, is assessed. RESULTS Results confirm a significant correlation between CKD273 and clinical kidney parameters as well as with eGFR decline. Patient stratification using CKD273 at baseline, show a trend toward attenuation of renal function loss in high CKD-risk patients treated with linagliptin. Moreover, characterized are linagliptin affected peptides of which the majority contained a DPP-4 target sequence. CONCLUSIONS AND CLINICAL RELEVANCE CKD273 is a promising tool for identifying patients at high risk for CKD progression and may unmask a potential of linagliptin to slow progressive kidney function loss in high CKD-risk patients. UPP characterization reveals a significant impact of linagliptin on urinary peptides.
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Affiliation(s)
- Justyna Siwy
- mosaiques-diagnostics GmbH, Rotenburger Str. 20, 30659, Hannover, Germany
| | - Thomas Klein
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riß, Germany
| | - Marcel Rosler
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88397, Biberach an der Riß, Germany
| | - Maximilian von Eynatten
- Boehringer Ingelheim International GmbH. KG, Binger Str. 173, 55216, Ingelheim am Rhein, Germany
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10
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Belczacka I, Pejchinovski M, Krochmal M, Magalhães P, Frantzi M, Mullen W, Vlahou A, Mischak H, Jankowski V. Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers. Proteomics Clin Appl 2018; 13:e1800111. [PMID: 30334612 DOI: 10.1002/prca.201800111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/16/2018] [Indexed: 12/20/2022]
Abstract
PURPOSE Urine is a rich source of potential biomarkers, including glycoproteins. Glycoproteomic analysis remains difficult due to the high heterogeneity of glycans. Nevertheless, recent advances in glycoproteomics software solutions facilitate glycopeptide identification and characterization. The aim is to investigate intact glycopeptides in the urinary peptide profiles of normal subjects using a novel PTM-centric software-Byonic. EXPERIMENTAL DESIGN The urinary peptide profiles of 238 normal subjects, previously analyzed using CE-MS and CE-MS/MS and/or LC-MS/MS, are subjected to glycopeptide analysis. Additionally, glycopeptide distribution is assessed in a set of 969 patients with five different cancer types: bladder, prostate and pancreatic cancer, cholangiocarcinoma, and renal cell carcinoma. RESULTS A total of 37 intact O-glycopeptides and 23 intact N-glycopeptides are identified in the urinary profiles of 238 normal subjects. Among the most commonly identified O-glycoproteins are Apolipoprotein C-III and insulin-like growth factor II, while titin among the N-glycoproteins. Further statistical analysis reveals that three O-glycopeptides and five N-glycopeptides differed significantly in their abundance among the different cancer types, comparing to normal subjects. CONCLUSIONS AND CLINICAL RELEVANCE Through the established glycoproteomics workflow, intact O- and N-glycopeptides in human urine are identified and characterized, providing novel insights for further exploration of the glycoproteome with respect to specific diseases.
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Affiliation(s)
- Iwona Belczacka
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany.,University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
| | | | | | | | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, G128QQ Glasgow, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation Academy of Athens (BRFAA), 11527 Athens, Greece
| | | | - Vera Jankowski
- University Hospital RWTH Aachen, Institute for Molecular Cardiovascular Research (IMCAR), 52074 Aachen, Germany
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11
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Bonomini M, Pieroni L, Di Liberato L, Sirolli V, Urbani A. Examining hemodialyzer membrane performance using proteomic technologies. Ther Clin Risk Manag 2017; 14:1-9. [PMID: 29296087 PMCID: PMC5739111 DOI: 10.2147/tcrm.s150824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The success and the quality of hemodialysis therapy are mainly related to both clearance and biocompatibility properties of the artificial membrane packed in the hemodialyzer. Performance of a membrane is strongly influenced by its interaction with the plasma protein repertoire during the extracorporeal procedure. Recognition that a number of medium-high molecular weight solutes, including proteins and protein-bound molecules, are potentially toxic has prompted the development of more permeable membranes. Such membrane engineering, however, may cause loss of vital proteins, with membrane removal being nonspecific. In addition, plasma proteins can be adsorbed onto the membrane surface upon blood contact during dialysis. Adsorption can contribute to the removal of toxic compounds and governs the biocompatibility of a membrane, since surface-adsorbed proteins may trigger a variety of biologic blood pathways with pathophysiologic consequences. Over the last years, use of proteomic approaches has allowed polypeptide spectrum involved in the process of hemodialysis, a key issue previously hampered by lack of suitable technology, to be assessed in an unbiased manner and in its full complexity. Proteomics has been successfully applied to identify and quantify proteins in complex mixtures such as dialysis outflow fluid and fluid desorbed from dialysis membrane containing adsorbed proteins. The identified proteins can also be characterized by their involvement in metabolic and signaling pathways, molecular networks, and biologic processes through application of bioinformatics tools. Proteomics may thus provide an actual functional definition as to the effect of a membrane material on plasma proteins during hemodialysis. Here, we review the results of proteomic studies on the performance of hemodialysis membranes, as evaluated in terms of solute removal efficiency and blood-membrane interactions. The evidence collected indicates that the information provided by proteomic investigations yields improved molecular and functional knowledge and may lead to the development of more efficient membranes for the potential benefit of the patient.
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Affiliation(s)
- Mario Bonomini
- Department of Medicine, G. d'Annunzio University, Chieti
| | - Luisa Pieroni
- Proteomic and Metabonomic Units, IRCCS S. Lucia Foundation, Rome
| | | | | | - Andrea Urbani
- Proteomic and Metabonomic Units, IRCCS S. Lucia Foundation, Rome.,Faculty of Medicine, Biochemistry and Clinical Biochemistry Institute, Catholic University of the "Sacred Heart", Rome, Italy
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12
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Cherney D, Perkins BA, Lytvyn Y, Heerspink H, Rodríguez-Ortiz ME, Mischak H. The effect of sodium/glucose cotransporter 2 (SGLT2) inhibition on the urinary proteome. PLoS One 2017; 12:e0186910. [PMID: 29084249 PMCID: PMC5662219 DOI: 10.1371/journal.pone.0186910] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/14/2017] [Indexed: 12/02/2022] Open
Abstract
Treatment with empagliflozin, an inhibitor of the sodium/glucose cotransporter 2 (SGLT2), is associated with slower progression of diabetic kidney disease. In this analysis, we explored the hypothesis that empagliflozin may have an impact on urinary peptides associated with chronic kidney disease (CKD). In this post-hoc, exploratory analysis, we investigated urine samples obtained from 40 patients with uncomplicated type 1 diabetes (T1D) before and after treatment with empagliflozin for 8 weeks to for significant post-therapy changes in urinary peptides. We further assessed the association of these changes with CKD in an independent cohort, and with a previously established urinary proteomic panel, termed CKD273. 107 individual peptides significantly changed after treatment. The majority of the empagliflozin-induced changes were in the direction of “CKD absent” when compare to patients with CKD and controls. A classifier consisting of these 107 peptides scored significantly different in controls, in comparison to CKD patients. However, empagliflozin did not impact the CKD273 classifier. Our data indicate that empagliflozin induces multiple significant changes in the urinary proteomic markers such as mucin and clusterin. The relationship between empagliflozin-induced proteomic changes and clinical outcomes merits further investigation.
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Affiliation(s)
- David Cherney
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - Bruce A. Perkins
- Division of Endocrinology, University Health Network, University of Toronto, Toronto, Canada
| | - Yuliya Lytvyn
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - Hiddo Heerspink
- Department of Clinical Pharmacology University Medical Center Groningen, Groningen, the Netherlands
| | - María E. Rodríguez-Ortiz
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz. Fundación Renal Iñigo Álvarez de Toledo. Universidad Autónoma de Madrid. REDinREN, Madrid, Spain
| | - Harald Mischak
- Mosaiques diagnostics GmbH, Hanover, Germany
- BHF Glasgow Cardiovascular Research Centre, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
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13
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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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14
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Bonomini M, Sirolli V, Pieroni L, Felaco P, Amoroso L, Urbani A. Proteomic Investigations into Hemodialysis Therapy. Int J Mol Sci 2015; 16:29508-21. [PMID: 26690416 PMCID: PMC4691132 DOI: 10.3390/ijms161226189] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/26/2015] [Accepted: 12/02/2015] [Indexed: 01/07/2023] Open
Abstract
The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane's performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane's bio(in)compatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research.
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Affiliation(s)
- Mario Bonomini
- Nephrology and Dialysis Institute, Department of Medicine, G. d'Annunzio University, Chieti-Pescara, SS. Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy.
| | - Vittorio Sirolli
- Nephrology and Dialysis Institute, Department of Medicine, G. d'Annunzio University, Chieti-Pescara, SS. Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy.
| | - Luisa Pieroni
- Proteomics and Metabonomics Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) S. Lucia Foundation, 00179 Rome, Italy.
- Department of Surgery and Experimental Medicine, Tor Vergata University, 00134 Rome, Italy.
| | - Paolo Felaco
- Nephrology and Dialysis Institute, Department of Medicine, G. d'Annunzio University, Chieti-Pescara, SS. Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy.
| | - Luigi Amoroso
- Nephrology and Dialysis Institute, Department of Medicine, G. d'Annunzio University, Chieti-Pescara, SS. Annunziata Hospital, Via dei Vestini, 66013 Chieti, Italy.
| | - Andrea Urbani
- Proteomics and Metabonomics Laboratory, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) S. Lucia Foundation, 00179 Rome, Italy.
- Department of Surgery and Experimental Medicine, Tor Vergata University, 00134 Rome, Italy.
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15
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Gopal J, Muthu M, Chun SC, Wu HF. State-of-the-art nanoplatform-integrated MALDI-MS impacting resolutions in urinary proteomics. Proteomics Clin Appl 2015; 9:469-81. [PMID: 25736343 DOI: 10.1002/prca.201400182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/26/2014] [Accepted: 02/26/2015] [Indexed: 12/17/2022]
Abstract
Urine proteomics has become a subject of interest, since it has led to a number of breakthroughs in disease diagnostics. Urine contains information not only from the kidney and the urinary tract but also from other organs, thus urinary proteome analysis allows for identification of biomarkers for both urogenital and systemic diseases. The following review gives a brief overview of the analytical techniques that have been in practice for urinary proteomics. MALDI-MS technique and its current application status in this area of clinical research have been discussed. The review comments on the challenges facing the conventional MALDI-MS technique and the upgradation of this technique with the introduction of nanotechnology. This review projects nano-based techniques such as nano-MALDI-MS, surface-assisted laser desorption/ionization, and nanostructure-initiator MS as the platforms that have the potential in trafficking MALDI-MS from the lab to the bedside.
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Affiliation(s)
- Judy Gopal
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Manikandan Muthu
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Se-Chul Chun
- Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
| | - Hui-Fen Wu
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan.,School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University and Academia Sinica, Kaohsiung, Taiwan.,Center for Nanosciences and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
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16
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Robledo VR, Smyth WF. Review of the CE-MS platform as a powerful alternative to conventional couplings in bio-omics and target-based applications. Electrophoresis 2014; 35:2292-308. [DOI: 10.1002/elps.201300561] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/24/2014] [Accepted: 01/24/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Virginia Rodríguez Robledo
- Faculty of Pharmacy; Department of Analytical Chemistry and Food Technology; University of Castilla-La Mancha (UCLM); Albacete Spain
| | - William Franklin Smyth
- School of Pharmacy and Pharmaceutical Sciences; University of Ulster; Coleraine Northern Ireland UK
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17
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Mullen W, Saigusa D, Abe T, Adamski J, Mischak H. Proteomics and Metabolomics as Tools to Unravel Novel Culprits and Mechanisms of Uremic Toxicity: Instrument or Hype? Semin Nephrol 2014; 34:180-90. [DOI: 10.1016/j.semnephrol.2014.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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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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19
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Stalmach A, Albalat A, Mullen W, Mischak H. Recent advances in capillary electrophoresis coupled to mass spectrometry for clinical proteomic applications. Electrophoresis 2013; 34:1452-64. [DOI: 10.1002/elps.201200708] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/07/2013] [Accepted: 02/14/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Angelique Stalmach
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | - Amaya Albalat
- Department of Proteomics and Systems Medicine; BHF Glasgow Cardiovascular Research Centre; Institute of Cardiovascular and Medical Sciences; College of Medical Veterinary and Life Sciences; University of Glasgow; Glasgow; UK
| | - William Mullen
- Department of Proteomics and Systems Medicine; 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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20
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Mischak H, Vlahou A, Ioannidis JP. Technical aspects and inter-laboratory variability in native peptide profiling: The CE–MS experience. Clin Biochem 2013; 46:432-43. [DOI: 10.1016/j.clinbiochem.2012.09.025] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/18/2012] [Accepted: 09/27/2012] [Indexed: 02/08/2023]
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21
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Hallbauer J, Kreusch S, Klemm A, Wolf G, Rhode H. Long-term serum proteomes are quite similar under high- and low-flux hemodialysis treatment. Proteomics Clin Appl 2010; 4:953-61. [DOI: 10.1002/prca.201000051] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 08/11/2010] [Accepted: 09/07/2010] [Indexed: 11/06/2022]
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22
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Proteomics in extracorporeal blood purification and peritoneal dialysis. J Proteomics 2010; 73:521-6. [DOI: 10.1016/j.jprot.2009.06.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 05/31/2009] [Accepted: 06/04/2009] [Indexed: 11/18/2022]
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23
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Mischak H, Espandiari P, Sadrieh N, Hanig J. Profiling of rat urinary proteomic patterns associated with drug-induced nephrotoxicity using CE coupled with MS as a potential model for detection of drug-induced adverse effects. Proteomics Clin Appl 2009; 3:1062-71. [PMID: 21137006 DOI: 10.1002/prca.200900030] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 04/15/2009] [Accepted: 05/05/2009] [Indexed: 11/06/2022]
Abstract
We have investigated urine obtained from Sprague Dawley rats before and after administration of cis-Platin, aiming at the definition of biomarkers for drug-induced cytotoxicity. Rats were treated with 3 or 6 mg/kg cis-Platin (i.p., single injection) and urine samples were collected before and after drug or saline treatment. Analysis of the low molecular weight proteome (<20 kDa) using capillary-electrophoresis coupled mass spectrometry allowed us to tentatively identify 34 urinary peptides that show significant differences between control and treated animals, and hence may serve as a potential biomarker for cis-Platin-induced nephrotoxicity. These biomarkers were confirmed in a blinded assessment of additional samples. The blinded data also revealed time-dependency of induced changes. Some of the potential biomarkers could be sequenced. This information revealed great similarity between cis-Platin-induced changes and significant changes in the urinary proteome of patients suffering from tubular injury (Fanconi syndrome). Our study strongly suggests that (drug-induced) nephrotoxicity can be detected with high accuracy in laboratory rodents using urinary proteome analysis. The effects observed are very similar to those seen in corresponding human diseases and similar approaches may be very helpful in evaluating drug-induced organ damage in preclinical animal models. This study aiming at the definition of biomarkers for drug-induced cytotoxicity may serve as a proof-of-principle for the use of urinary proteomics in assessment of drug-induced nephrotoxicity.
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24
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Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
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25
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26
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Staub A, Schappler J, Rudaz S, Veuthey JL. CE-TOF/MS: Fundamental concepts, instrumental considerations and applications. Electrophoresis 2009; 30:1610-23. [DOI: 10.1002/elps.200800782] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Kistler AD, Mischak H, Poster D, Dakna M, Wüthrich RP, Serra AL. Identification of a unique urinary biomarker profile in patients with autosomal dominant polycystic kidney disease. Kidney Int 2009; 76:89-96. [PMID: 19340089 DOI: 10.1038/ki.2009.93] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
To gain some insight into early disease progression in human autosomal dominant polycystic kidney disease (ADPKD), we analyzed the urine proteome of 41 young patients with ADPKD whose renal function was relatively preserved. Using capillary electrophoresis and mass spectrometry, we compared these results to those from age-matched healthy controls and patients with other renal diseases. There were 197 proteins with significantly altered urinary excretion; and 38 of them could be sequenced, most of which were collagen fragments. This suggests that there is high turnover of extracellular matrix proteins. Uromodulin peptides, previously implicated in tubular injury, were also found in the urine specimens. These marker proteins were found to distinguish patients from controls with a high degree of accuracy. The sensitivity and specificity of this marker set remained high in an independent validation cohort of 24 patients with ADPKD and 35 healthy controls, and even in comparisons of patients with a variety of other renal diseases or patients with kidney or bladder cancer. These findings present a potential hypothesis for the mechanisms of disease progression in ADPKD which will need to be confirmed by further studies.
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28
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Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G. Approaching clinical proteomics: current state and future fields of application in fluid proteomics. Clin Chem Lab Med 2009; 47:724-44. [DOI: 10.1515/cclm.2009.167] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Metzger J, Luppa PB, Good DM, Mischak H. Adapting mass spectrometry-based platforms for clinical proteomics applications: The capillary electrophoresis coupled mass spectrometry paradigm. Crit Rev Clin Lab Sci 2009; 46:129-52. [PMID: 19404829 PMCID: PMC5769463 DOI: 10.1080/10408360902805261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Single biomarker detection is common in clinical laboratories due to the currently available method spectrum. For various diseases, however, no specific single biomarker could be identified. A strategy to overcome this diagnostic void is to shift from single analyte detection to multiplexed biomarker profiling. Mass spectrometric methods were employed for biomarker discovery in body fluids. The enormous complexity of biofluidic proteome compartments implies upstream fractionation. For this reason, mass spectrometry (MS) was coupled to two-dimensional gel electrophoresis, liquid chromatography, surface-enhanced laser desorption/ionization, or capillary electrophoresis (CE). Differences in performance and operating characteristics make them differentially suited for routine laboratory applications. Progress in the field of clinical proteomics relies not only on the use of an adequate technological platform, but also on a fast and efficient proteomic workflow including standardized sample preparation, proteomic data processing, statistical validation of biomarker selection, and sample classification. Based on CE-MS analysis, we describe how proteomic technology can be implemented in a clinical laboratory environment. In the last part of this review, we give an overview of CE-MS-based clinical studies and present information on identity and biological significance of the identified peptide biomarkers providing evidence of disease-induced changes in proteolytic processing and posttranslational modification.
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Affiliation(s)
- Jochen Metzger
- Mosaiques Diagnostics and Terapeutics AG, Mellendorfer Str. 7-9, Hannover 30625, Germany.
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30
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Pantůčková P, Gebauer P, Boček P, Křivánková L. Electrolyte systems for on-line CE-MS: Detection requirements and separation possibilities. Electrophoresis 2009; 30:203-14. [DOI: 10.1002/elps.200800262] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Dihazi H, Müller CA, Mattes H, Müller GA. Proteomic analysis to improve adequacy of hemo- and peritoneal dialysis: Removal of small and high molecular weight proteins with high- and low-flux filters or a peritoneal membrane. Proteomics Clin Appl 2008; 2:1167-82. [DOI: 10.1002/prca.200780143] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Indexed: 11/08/2022]
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32
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Herrero M, Ibañez E, Cifuentes A. Capillary electrophoresis-electrospray-mass spectrometry in peptide analysis and peptidomics. Electrophoresis 2008; 29:2148-60. [DOI: 10.1002/elps.200700404] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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33
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Balgley BM, Wang W, Fang X, DeVoe DL, Lee CS. Capillary Electrophoretic Separations for Clinical Proteomics. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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34
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Schiffer E, Mischak H, Vanholder RC. Biomarkers for Renal Disease and Uremic Toxins. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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35
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Schiffer E, Mischak H, Theodorescu D, Vlahou A. Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform. World J Urol 2008; 26:67-74. [PMID: 18175124 DOI: 10.1007/s00345-007-0234-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 12/11/2007] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Bladder cancer (BCa) is one of the most prevalent malignancies worldwide, mostly due to its high recurrence rates. In consequence, the necessity of repeated screening for reappearance demonstrates the urgent need for novel biomarkers as alternatives to invasive standard procedures. METHODS Proteomic technologies have emerged as powerful platforms for unbiased biomarker discovery and revolutionized the classical "target-driven" analysis of single marker candidates. Although proteome profiling is still far from demonstrating its full potential in clinical diagnosis, first studies clearly denote its significant potential. CONCLUSIONS This review provides a discussion of the challenges related to clinical proteomics using mass spectrometry, emphasizing bladder cancer biomarker discovery. An outline of the technological prerequisites for reliable proteome profiling, data mining and interpretation, as well as, reflections on future trends in the field are provided.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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36
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Haselberg R, de Jong GJ, Somsen GW. Capillary electrophoresis–mass spectrometry for the analysis of intact proteins. J Chromatogr A 2007; 1159:81-109. [PMID: 17560583 DOI: 10.1016/j.chroma.2007.05.048] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/01/2007] [Accepted: 05/15/2007] [Indexed: 10/23/2022]
Abstract
Developments in the fields of protein chemistry, proteomics and biotechnology have increased the demand for suitable analytical techniques for the analysis of intact proteins. In 1989, capillary electrophoresis (CE) was combined with mass spectrometry (MS) for the first time and its potential usefulness for the analysis of intact (i.e. non-digested) proteins was shown. This article provides an overview of the applications of CE-MS within the field of intact protein analysis. The principles of the applied CE modes and ionization techniques used for CE-MS of intact proteins are shortly described. It is shown that separations are predominantly carried out by capillary zone electrophoresis and capillary isoelectric focusing, whereas electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) are the most popular ionization techniques used for interfacing. The combination of CE with inductively coupled plasma (ICP) MS for the analysis of metalloproteins is also discussed. The various CE-MS combinations are systematically outlined and tables provide extensive overviews of the applications of each technique for intact protein analysis. Selected examples are given to illustrate the usefulness of the CE-MS techniques. Examples include protein isoform assignment, single cell analysis, metalloprotein characterization, proteomics and biomarker screening. Finally, chip-based electrophoresis combined with MS is shortly treated and some of its applications are described. It is concluded that CE-MS represents a powerful tool for the analysis of intact proteins yielding unique separations and information.
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Affiliation(s)
- Rob Haselberg
- Department of Biomedical Analysis, Utrecht University, 3508 TB Utrecht, The Netherlands.
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37
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Thongboonkerd V. Recent progress in urinary proteomics. Proteomics Clin Appl 2007; 1:780-91. [PMID: 21136734 DOI: 10.1002/prca.200700035] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2007] [Indexed: 11/08/2022]
Abstract
Urinary proteomics has become one of the most attractive subdisciplines in clinical proteomics as the urine is an ideal source for the discovery of noninvasive biomarkers for kidney and nonkidney diseases. This field has been growing rapidly as indicated by >80 original research articles on urinary proteome analyses appearing since 2001, of which 28 (approximately 1/3) had been published within the year 2006. The most common technologies used in recent urinary proteome studies remain gel-based methods (1-DE, 2-DE and 2-D DIGE), whereas LC-MS/MS, SELDI-TOF MS, and CE-MS are other commonly used techniques. In addition, mass spectrometric immunoassay (MSIA) and array technology have also been applied. This review provides an extensive but concise summary of recent applications of urinary proteomics. Proteomic analyses of dialysate and ultrafiltrate fluids derived from renal replacement therapy (or artificial kidney) are also discussed.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Molecular Biology Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand. ,
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38
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Mischak H, Julian BA, Novak J. High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine. Proteomics Clin Appl 2007; 1:792. [PMID: 20107618 PMCID: PMC2811330 DOI: 10.1002/prca.200700043] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Indexed: 11/09/2022]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
| | | | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
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39
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Frommberger M, Zürbig P, Jantos J, Krahn T, Mischak H, Pich A, Just I, Schmitt-Kopplin P, Schiffer E. Peptidomic analysis of rat urine using capillary electrophoresis coupled to mass spectrometry. Proteomics Clin Appl 2007; 1:650-60. [PMID: 21136720 DOI: 10.1002/prca.200700195] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Indexed: 11/10/2022]
Abstract
We have established and validated a protocol for the peptidomic analysis of rat urine using CE coupled to MS (CE-MS). In the first experiments, the reproducibility of the CE-MS set-up and of the established preparation procedure were assessed. To establish a first rat urinary peptidome map, samples were also analyzed using CE-FT-ICR. The subsequent analysis of independent samples from two different strains (WISTAR and CD) indicated strain-specific differences, which were validated in a blinded assessment. MS/MS revealed the presence of specific fragments from well-known urinary rat peptides, such as collagens, alpha-1-antitrypsin, and serum albumin. The CE-MS-based peptidomics platform may provide novel insights into body fluids of animal models, such as rat or mice. Together with peptide identification, the technology appears to be an excellent, complimentary, and non-invasive tool to analyze toxicological or other (patho)physiological effects of pharmaceutical compounds in animal models.
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Affiliation(s)
- Moritz Frommberger
- Institute of Ecological Chemistry, GSF - National Research Center for Environment and Health, Neuherberg, Germany
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40
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Sniehotta M, Schiffer E, Zürbig P, Novak J, Mischak H. CE – a multifunctional application for clinical diagnosis. Electrophoresis 2007; 28:1407-17. [PMID: 17427258 DOI: 10.1002/elps.200600581] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
CE has been used widely as an analytical tool with high separation power taking advantage of size, charge-to-size ratio, or isoelectric point of various analytes. In combination with detection methods, such as UV absorption, electrochemical detection, fluorescence, or mass spectrometry (MS), it allows the separation and detection of inorganic and organic ions, as well as complex compounds, such as polypeptides, nucleic acids, including PCR amplicons from viruses or bacteria. Recent interest in identification of biomarkers of diseases using body fluids leads to development of CE-MS techniques. These applications allowed identification of new potential biomarkers for clinical diagnosis and monitoring of therapeutic interventions. In this report, we present a technical overview of various CE techniques and discuss their applications in clinical medicine.
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Affiliation(s)
- Maike Sniehotta
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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41
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Abstract
A new method for displaying CE-MALDI-MS data for proteolytic digests is described. This data display mode yields distinct charge-based trends for plots of mass-to-charge (m/z) versus CE migration time. These trends arise owing to the in-solution charge state of the peptides, and this interpretation was confirmed by using empirical peptide electromigration models and peptide standards as charge-state markers. These charge-state specific trends exhibit analytical utility by providing additional chemical information about the peptides, which increases the confidence level of peptide identification and provides a rapid means for screening for posttranslationally modified peptides.
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Affiliation(s)
- Brad J Williams
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
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42
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Bodzon-Kulakowska A, Bierczynska-Krzysik A, Dylag T, Drabik A, Suder P, Noga M, Jarzebinska J, Silberring J. Methods for samples preparation in proteomic research. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:1-31. [PMID: 17113834 DOI: 10.1016/j.jchromb.2006.10.040] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2006] [Accepted: 10/23/2006] [Indexed: 01/04/2023]
Abstract
Sample preparation is one of the most crucial processes in proteomics research. The results of the experiment depend on the condition of the starting material. Therefore, the proper experimental model and careful sample preparation is vital to obtain significant and trustworthy results, particularly in comparative proteomics, where we are usually looking for minor differences between experimental-, and control samples. In this review we discuss problems associated with general strategies of samples preparation, and experimental demands for these processes.
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Affiliation(s)
- Anna Bodzon-Kulakowska
- Department of Neurobiochemistry, Faculty of Chemistry, Jagiellonian University, Ingardena St. 3, 30-060 Krakow, Poland
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43
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Fliser D, Novak J, Thongboonkerd V, Argilés A, Jankowski V, Girolami MA, Jankowski J, Mischak H. Advances in urinary proteome analysis and biomarker discovery. J Am Soc Nephrol 2007; 18:1057-71. [PMID: 17329573 DOI: 10.1681/asn.2006090956] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Noninvasive diagnosis of kidney diseases and assessment of the prognosis are still challenges in clinical nephrology. Definition of biomarkers on the basis of proteome analysis, especially of the urine, has advanced recently and may provide new tools to solve those challenges. This article highlights the most promising technological approaches toward deciphering the human proteome and applications of the knowledge in clinical nephrology, with emphasis on the urinary proteome. The data in the current literature indicate that although a thorough investigation of the entire urinary proteome is still a distant goal, clinical applications are already available. Progress in the analysis of human proteome in health and disease will depend more on the standardization of data and availability of suitable bioinformatics and software solutions than on new technological advances. It is predicted that proteomics will play an important role in clinical nephrology in the very near future and that this progress will require interactive dialogue and collaboration between clinicians and analytical specialists.
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Affiliation(s)
- Danilo Fliser
- Mosaiques Diagnostics and Therapeutics AG, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
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44
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Abstract
Rheumatology abounds in diseases that are relatively poorly understood or diseases that are not easily managed clinically. Recently DNA microarray and proteomic-based approaches have made steady inroads into the study of various rheumatic diseases. Herein we review recent proteomic approaches that have been applied to the study of rheumatic diseases. These methods include two-dimensional gel electrophoresis/mass spectrometry (MS), multidimensional high-pressure liquid chromatography-MS/MS, capillary electrophoresis-MS/MS, surface-enhanced laser desorption/ionization-time of flight-MS/MS, and a variety of targeted antibody-based protein arrays. Although each of these different methods has its own advantages and disadvantages, the application of these proteomic tools to rheumatology has given birth to a steadily increasing panel of molecules that may have the potential to serve as early biomarkers in various rheumatic diseases.
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Affiliation(s)
- Tianfu Wu
- Department of Internal Medicine (Rheumatology), University of Texas Southwestern Medical School, Dallas, Texas 75390-8884, USA.
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45
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Weissinger EM, Hertenstein B, Mischak H, Ganser A. Online coupling of capillary electrophoresis with mass spectrometry for the identification of biomarkers for clinical diagnosis. Expert Rev Proteomics 2006; 2:639-47. [PMID: 16209644 DOI: 10.1586/14789450.2.5.639] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteomic screening of complex biologic samples is of increasing importance in clinical research and diagnosis. In the postgenomic area it is evident that changes of the composition of body fluids, as well as post-translational modifications of proteins and peptides, provide more information than genetic typing. The study of these changes allows the state of health or disease of particular organs, and consequently, the whole organism, to be described. This review describes the application of capillary electrophoresis coupled online to an electrospray ionization time-of-flight mass spectrometer to the analysis of body fluids obtained from patients for the identification of biomarkers for diagnostic purposes.
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Affiliation(s)
- Eva M Weissinger
- Department of Hematology, Hemostasis & Oncology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
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46
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Abstract
Proteomic technologies are used with increasing frequency in the renal community. In this review, we highlight the use in renal research of a number of available techniques including two-dimensional gel electrophoresis, liquid chromatography/mass spectrometry, surface-enhanced laser desorption/ionization, capillary electrophoresis/mass spectrometry, and antibody and tissue arrays. These techniques have been used to identify proteins or changes in proteins specific to regions of the kidney or associated with renal diseases or toxicity. They have also been used to examine protein expression changes and posttranslational modifications of proteins during signaling. A number of studies have used proteomic methodologies to look for diagnostic biomarkers in body fluids. The rapid rate of development of the technologies along with the combination of classic physiological and biochemical techniques with proteomics will enable new discoveries.
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Affiliation(s)
- Michael G Janech
- Medical University of South Carolina, Ralph H. Johnson Veterans Affairs Medical Center, Charleston, SC 29425-2220, USA
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47
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Hernández-Borges J, Borges-Miquel TM, Rodríguez-Delgado MA, Cifuentes A. Sample treatments prior to capillary electrophoresis-mass spectrometry. J Chromatogr A 2006; 1153:214-26. [PMID: 17098242 DOI: 10.1016/j.chroma.2006.10.070] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 10/13/2006] [Accepted: 10/30/2006] [Indexed: 10/23/2022]
Abstract
Sample preparation is a crucial part of chemical analysis and in most cases can become the bottleneck of the whole analytical process. Its adequacy is a key factor in determining the success of the analysis and, therefore, careful selection and optimization of the parameters controlling sample treatment should be carried out. This work revises the different strategies that have been developed for sample preparation prior to capillary electrophoresis-mass spectrometry (CE-MS). Namely the present work presents an exhaustive and critical revision of the different samples treatments used together with on-line CE-MS including works published from January 2000 to July 2006.
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Affiliation(s)
- Javier Hernández-Borges
- Department of Analytical Chemistry, Nutrition and Food Science, University of La Laguna, Avda. Astrofísico Fco. Sánchez s/n, 38071 La Laguna, Tenerife, Spain.
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48
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Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics 2006; 6:5615-27. [PMID: 16991199 DOI: 10.1002/pmic.200600230] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance both diagnosis and therapy of specific diseases. Proteomic methods can provide means to accomplish this grand medical vision. In this review, we will focus on the potential use of proteome analysis for clinical applications, such as disease diagnosis and assessment of response to therapy. We focus on CE coupled with MS (CE-MS) and review in detail different aspects of CE-MS coupling and the results obtained using CE-MS analysis of clinically relevant samples. We also discuss clinical applications of the technology for the diagnosis of renal diseases, urogenital cancer, and arteriosclerosis as well as monitoring the responses to therapeutic interventions.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics & Therapeutics AG, Hanover, Germany
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49
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Huang YF, Huang CC, Hu CC, Chang HT. Capillary electrophoresis-based separation techniques for the analysis of proteins. Electrophoresis 2006; 27:3503-22. [PMID: 16927348 DOI: 10.1002/elps.200600100] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
CE offers the advantages of high speed, great efficiency, as well as the requirement of minimum amounts of sample and buffer for the analysis of proteins. In this review, we summarize the CE-based techniques coupled with absorption, LIF, and MS detection systems for the analysis of proteins mostly within the past 5 years. The basic principle of each technique and its advantages and disadvantages for protein analysis are discussed in brief. Advanced CE techniques, including on-column concentration techniques and high-efficiency multidimensional separation techniques, for high-throughput protein profiling of complex biological samples and/or of single cells are emphasized. Although the developed techniques provide improved peak capacity, they have not become practical tools for proteomics, mainly because of poor reproducibility, low-sample lading capacity, and low throughput due to ineffective interfaces between two separation dimensions and that between separation and MS systems. In order to identify the complexities and dynamics of the proteomes expressed by cells, tissues, or organisms, techniques providing improved analytical sensitivity, throughput, and dynamic ranges are still demanded.
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Affiliation(s)
- Yu-Fen Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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50
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Servais AC, Crommen J, Fillet M. Capillary electrophoresis-mass spectrometry, an attractive tool for drug bioanalysis and biomarker discovery. Electrophoresis 2006; 27:2616-29. [PMID: 16817163 DOI: 10.1002/elps.200500934] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The coupling of CE with MS detection, a relatively recent hyphenated technique, has gained increasing respect in the field of bioanalytical applications over the past few years. The first part of this review presents CE-MS applications dealing with drug bioanalysis, including forensic analysis and metabolism studies. Practical considerations to achieve a robust and sensitive CE-MS coupling are also presented. It is indeed essential to strictly control some critical electrospray parameters, such as the sheath liquid composition and flow rate, the nebulizing gas pressure as well as the capillary outlet position. The second part of the review critically describes the applications of CE coupled on-line to MS for the identification of biomarkers in body fluids for diagnostic purposes. Since the sample preparation procedures strongly differ according to the intended use (drug bioanalysis or biomarker discovery), they are discussed separately, taking into account the particular properties of plasma and urine matrices.
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Affiliation(s)
- Anne-Catherine Servais
- Department of Analytical Pharmaceutical Chemistry, Institute of Pharmacy, University of Liège, Belgium
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