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      Proteomics in Nephrology: Current Status and Future Directions

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          Abstract

          Proteomics is one among various ‘OMICS’ fields that have been growing rapidly in the postgenomic era. During the past few years, proteomics has been extensively applied to several fields of medicine to better understand normal physiology, to define the pathophysiology of diseases, and to identify novel biomarkers and new therapeutic targets. This review focuses on current status and future directions of proteomics in the nephrology field. Recent studies of renal proteome, proteomes of individual intrarenal structures (i.e., glomerular, vascular, tubular, brush border membrane, mesangial, and podocyte proteomes), urinary proteome, and protein profiles in dialysate or ultrafiltrate removed by renal replacement therapy are summarized.

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          A generic protein purification method for protein complex characterization and proteome exploration.

          G Rigaut, A. Shevchenko, B Rutz … (1999)
          We have developed a generic procedure to purify proteins expressed at their natural level under native conditions using a novel tandem affinity purification (TAP) tag. The TAP tag allows the rapid purification of complexes from a relatively small number of cells without prior knowledge of the complex composition, activity, or function. Combined with mass spectrometry, the TAP strategy allows for the identification of proteins interacting with a given target protein. The TAP method has been tested in yeast but should be applicable to other cells or organisms.
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            Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling.

            Tony Hunter (1995)
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              Use of proteomic patterns in serum to identify ovarian cancer.

              Emanuel Petricoin, Ali M. Ardekani, Ben Hitt … (2002)
              New technologies for the detection of early-stage ovarian cancer are urgently needed. Pathological changes within an organ might be reflected in proteomic patterns in serum. We developed a bioinformatics tool and used it to identify proteomic patterns in serum that distinguish neoplastic from non-neoplastic disease within the ovary. Proteomic spectra were generated by mass spectroscopy (surface-enhanced laser desorption and ionisation). A preliminary "training" set of spectra derived from analysis of serum from 50 unaffected women and 50 patients with ovarian cancer were analysed by an iterative searching algorithm that identified a proteomic pattern that completely discriminated cancer from non-cancer. The discovered pattern was then used to classify an independent set of 116 masked serum samples: 50 from women with ovarian cancer, and 66 from unaffected women or those with non-malignant disorders. The algorithm identified a cluster pattern that, in the training set, completely segregated cancer from non-cancer. The discriminatory pattern correctly identified all 50 ovarian cancer cases in the masked set, including all 18 stage I cases. Of the 66 cases of non-malignant disease, 63 were recognised as not cancer. This result yielded a sensitivity of 100% (95% CI 93--100), specificity of 95% (87--99), and positive predictive value of 94% (84--99). These findings justify a prospective population-based assessment of proteomic pattern technology as a screening tool for all stages of ovarian cancer in high-risk and general populations.
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                Author and article information

                Journal
                Journal ID (publisher-id): AJN
                Journal ID (nlm-ta): Am J Nephrol
                Journal ID (doi): 10.1159/issn.0250-8095
                Title: American Journal of Nephrology
                Publisher: S. Karger AG
                ISSN (Print): 0250-8095
                ISSN (Electronic): 1421-9670
                Publication date Subscription-year: 2004
                Publication date (Print): June 2004
                Publication date (Electronic): 06 July 2004
                Volume: 24
                Issue: 3
                Pages: 360-378
                Affiliations
                Siriraj Proteomics Center, Medical Molecular Biology Unit, Office for Research and Development, Faculty of Medicine at Siriraj Hospital, Mahidol University, Bangkok, Thailand
                Article
                Publisher ID: 79148 Other ID: Am J Nephrol 2004;24:360–378
                DOI: 10.1159/000079148
                PubMed ID: 15205555
                SO-VID: 6c5786d7-ee41-4908-a78d-e9784c4dddf7
                Copyright © © 2004 S. Karger AG, Basel
                License:

                Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher. Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.

                History
                Date received : 23 April 2004
                Date accepted : 24 May 2004
                Page count
                Figures: 6, Tables: 1, References: 135, Pages: 19
                Categories
                Subject: In-Depth Topic Review

                ScienceOpen disciplines: Cardiovascular Medicine,Nephrology
                Keywords: Proteomics,Biomarkers,Disease,Proteomic analysis,Proteome,Physiology, nephrology,Mass spectrometry
                Data availability:
                ScienceOpen disciplines: Cardiovascular Medicine, Nephrology
                Keywords: Proteomics, Biomarkers, Disease, Proteomic analysis, Proteome, Physiology, nephrology, Mass spectrometry

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