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Goëb V, Thomas-L'Otellier M, Daveau R, Charlionet R, Fardellone P, Le Loët X, Tron F, Gilbert D, Vittecoq O. Candidate autoantigens identified by mass spectrometry in early rheumatoid arthritis are chaperones and citrullinated glycolytic enzymes. Arthritis Res Ther 2009; 11:R38. [PMID: 19284558 PMCID: PMC2688184 DOI: 10.1186/ar2644] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 01/26/2009] [Accepted: 03/10/2009] [Indexed: 12/30/2022] Open
Abstract
Introduction The aim of our study was to identify new early rheumatoid arthritis (RA) autoantibodies. Methods Sera obtained from 110 early untreated RA patients (<6 months) were analyzed by western blot using HL-60 cell extract, separated on one-dimensional and two-dimensional gel electrophoresis (1-DE, 2-DE). Sera from 50 healthy blood donors and 20 patients with non-RA rheumatisms were used as controls for 1-DE and 2-DE, respectively. The immunoreactive proteins were identified by MALDI-TOF mass spectrometric analysis and the presence of potential sites of citrullination in each of these proteins was evaluated. FT-ICR mass spectrometry was used to verify experimentally the effect of citrullination upon the mass profile observed by MALDI-TOF analysis. Results The 110 1-DE patterns allowed detection of 10 recurrent immunoreactive bands of 33, 39, 43, 46, 51, 54, 58, 62, 67 and 70 kDa, which were further characterized by 2-DE and proteomic analysis. Six proteins were already described RA antigens: heterogeneous nuclear ribonucleoprotein A2/B1, aldolase, α-enolase, calreticulin, 60 kDa heat shock protein (HSP60) and BiP. Phosphoglycerate kinase 1 (PGK1), stress-induced phosphoprotein 1 and the far upstream element-binding proteins (FUSE-BP) 1 and 2 were identified as new antigens. Post-translational protein modifications were analyzed and potentially deiminated peptides were found on aldolase, α-enolase, PGK1, calreticulin, HSP60 and the FUSE-BPs. We compared the reactivity of RA sera with citrullinated and noncitrullinated α-enolase and FUSE-BP linear peptides, and showed that antigenicity of the FUSE-BP peptide was highly dependent on citrullination. Interestingly, the anti-cyclic citrullinated peptide antibody (anti-CCP2) status in RA serum at inclusion was not correlated to the reactivity directed against FUSE-BP citrullinated peptide. Conclusions Two categories of antigens, enzymes of the glycolytic family and molecular chaperones are also targeted by the early untreated RA autoantibody response. For some of them, and notably the FUSE-BPs, citrullination is involved in the immunological tolerance breakdown observed earlier in RA patients. Autoantibodies recognizing a citrullinated peptide from FUSE-BP may enhance the sensibility for RA of the currently available anti-CCP2 test.
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Affiliation(s)
- Vincent Goëb
- Department of Rheumatology and Inserm Unit 905, IFRMP 23, Institute for Biomedical Research, University of Rouen, Rouen University Hospital, Rouen 76031 cedex, France.
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Dwivedi RC, Dhindsa N, Krokhin OV, Cortens J, Wilkins JA, El-Gabalawy HS. The effects of infliximab therapy on the serum proteome of rheumatoid arthritis patients. Arthritis Res Ther 2009; 11:R32. [PMID: 19265537 PMCID: PMC2688177 DOI: 10.1186/ar2637] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/25/2009] [Accepted: 03/06/2009] [Indexed: 12/31/2022] Open
Abstract
Introduction Although the clinical effects of infliximab therapy in rheumatoid arthritis have been documented extensively, the biological effects of this intervention continue to be defined. We sought to examine the impact of infliximab therapy on the serum proteome of rheumatoid arthritis patients by means of a mass spectrometry-based approach. Methods Sera from 10 patients with rheumatoid arthritis were obtained prior to and following 12 weeks of infliximab therapy using a standard clinical protocol. The sera were immunodepleted of the 12 highest abundance proteins, labeled by the iTRAQ (isobaric tagging for relative and absolute protein quantification) technique, and analyzed by mass spectrometry to identify proteomic changes associated with treatment. Results An average of 373 distinct proteins were identified per patient with greater than 95% confidence. In the 3 patients demonstrating the most robust clinical responses, changes of greater than 20% in the serum levels were observed in 39 proteins following treatment. The majority of these proteins were regulated directly or indirectly by tumour necrosis factor-alpha (TNF-α) and nuclear factor-kappa-B, with acute-phase proteins being uniformly down-regulated. A number of proteins, including members of the SERPIN family and S100A8, were down-regulated irrespective of clinical response. Conclusions The present study demonstrates that a robust clinical response to infliximab is associated with the down-regulation of a spectrum of serum proteins regulated by TNF-α, and provides a possible basis for defining the broader biological effects of the treatment in vivo.
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Affiliation(s)
- Ravi C Dwivedi
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada.
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Li YZ, Hu CJ, Leng XM, Zhao GF, Li N, Xu Y. Promising Diagnostic Biomarkers for Primary Biliary Cirrhosis Identified With Magnetic Beads and MALDI-TOF-MS. Anat Rec (Hoboken) 2009; 292:455-60. [PMID: 19248174 DOI: 10.1002/ar.20870] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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López-Pedrera C, Barbarroja N, Villalba JM. Novel biomarkers of atherosclerosis and cardiovascular risk in autoimmune diseases: Genomics and proteomics approaches. Proteomics Clin Appl 2009; 3:213-25. [DOI: 10.1002/prca.200800147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Indexed: 01/15/2023]
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Camafeita E, Lamas JR, Calvo E, López JA, Fernández-Gutiérrez B. Proteomics: New insights into rheumatic diseases. Proteomics Clin Appl 2009; 3:226-241. [DOI: 10.1002/prca.200800146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Dai Y, Hu C, Huang Y, Huang H, Liu J, Lv T. A proteomic study of peripheral blood mononuclear cells in systemic lupus erythematosus. Lupus 2009; 17:799-804. [PMID: 18755861 DOI: 10.1177/0961203308089444] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Our objective was to analyze the changes in the protein expression profiles of peripheral blood mononuclear cells (PBMCs) in patients with systemic lupus erythematosus (SLE). Peripheral blood was obtained from patients with SLE and healthy controls. 2-D gel electrophoresis was performed, and gels were silver-stained. Differentially expressed protein spots were detected, some of which were identified by MALDI-TOF spectrometry. Match rates of 71% +/- 4% and 72% +/- 4% were gotten for control and patient gels, respectively. 791 +/- 17 spots were detected for control gels and 781 +/- 17 for patient gels. Eleven protein spots were up-regulated, and 9 protein spots were down-regulated in patients with SLE. Five differentially expressed proteins were identified as immunoglobulin J chain, apolipoprotein A-IV precursor, calprotectin L1H and zinc finger protein subfamily 1A (all up-regulated) and glutathione S-transferase (down-regulated), some of which had previously been shown to play a potential role in the pathogenesis of SLE. We conclude there are significant changes in the 2-D maps of PBMCs in patients with SLE and applying this proteomic approach may be a useful way to gain novel insights into SLE.
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Affiliation(s)
- Y Dai
- The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Guangdong Province, China.
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Time course proteomic profile of rat acute myocardial infarction by SELDI-TOF MS analysis. Int J Cardiol 2009; 131:225-33. [DOI: 10.1016/j.ijcard.2007.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 08/30/2007] [Accepted: 10/20/2007] [Indexed: 11/21/2022]
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Fabien N, Goetz J, Sordet C, Humbel RL, Sibilia J. [New autoanti-bodies in rheumatoid arthritis: anti-citrullinated protein or peptide autoanti-bodies and the others]. Presse Med 2008; 37:1756-66. [PMID: 18951757 DOI: 10.1016/j.lpm.2008.06.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 03/07/2008] [Accepted: 06/19/2008] [Indexed: 10/21/2022] Open
Abstract
New treatment strategies require that rheumatoid arthritis (RA) be diagnosed as early as possible. New diagnostic markers were required, because rheumatoid factors (RF), until now criteria for classification of RA, are not sufficiently specific and sometimes appear late, thereby limiting their diagnostic usefulness. The objective of this review is to describe the current state of knowledge and more particularly to analyze the interest of new RA autoanti-bodies, called anti-peptide or anti-citrullinated protein anti-bodies (ACPA). Other autoanti-bodies have been described, including anti-Sa, anti-alpha enolase, and anti-calpastatin autoanti-bodies. Nonetheless, their diagnostic value remains limited compared to ACPA. Accordingly, in daily practice today, the only autoanti-bodies that must be tested for to diagnose RA are the ACPAs and RFs. The discovery of ACPA (initially called anti-keratin and anti-perinuclear anti-bodies) was a major step forward for the laboratory diagnosis of RA. The tests most often used routinely areenzyme-linked immunosorbent assays(ELISA) with cyclic citrullinated peptides, whence the name anti-CCP autoanti-bodies. Accordingly, the two terms ACPA and anti-CCP can both be used. The diagnostic value, in particular their specificity, is on the order of 95%, regardless of the method of identification. These markers are very useful and are often present earlier than RF. These ACPA also have prognostic value because they are associated with more aggressive forms of RA. On the other hand, their value over time, in particular, their fluctuation as a function of treatment, is more controversial. In practice, it is recommended to test for both RF and ACPA in a diagnostic work-up for early RA. During follow-up, the value of testing for these autoanti-bodies has not been demonstrated, but additional studies are still necessary with the anti-CCP autoanti-bodies and the new anti-citrullinated protein autoanti-bodies.
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Affiliation(s)
- Nicole Fabien
- Laboratoire d'auto-immunité, Hospices Civils de Lyon, Centre hospitalier Lyon-Sud, F-69495 Pierre Bénite Cedex, France
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Trocmé C, Marotte H, Baillet A, Pallot-Prades B, Garin J, Grange L, Miossec P, Tebib J, Berger F, Nissen MJ, Juvin R, Morel F, Gaudin P. Apolipoprotein A-I and platelet factor 4 are biomarkers for infliximab response in rheumatoid arthritis. Ann Rheum Dis 2008; 68:1328-33. [PMID: 18664547 DOI: 10.1136/ard.2008.093153] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
OBJECTIVES The use of biologicals such as infliximab has dramatically improved the treatment of rheumatoid arthritis (RA). However, factors predictive of therapeutic response need to be identified. A proteomic study was performed prior to infliximab therapy to identify a panel of candidate protein biomarkers of RA predictive of treatment response. METHODS Plasma profiles of 60 patients with RA (28 non-responders (as defined by the American College of Rheumatology 20% improvement criteria (ACR20)) negative and 32 responders (ACR70 positive) to infliximab) were studied by surface enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS) technology on two types of arrays, an anion exchange array (SAX2) and a nickel affinity array (IMAC3-Ni). Biomarker characterisation was carried out using classical biochemical methods (purification by ammonium sulfate precipitation or metal affinity chromatography) and identification by matrix assisted laser desorption/ionisation time-of-flight (MALDI-TOF) MS analysis. RESULTS Two distinct protein profiles were observed on both arrays and several proteins were differentially expressed in both patient populations. Five proteins at 3.86, 7.77, 7.97, 8.14 and 74.07 kDa were overexpressed in the non-responder group, whereas one at 28 kDa was increased in the responder population (sensitivity>56%, specificity>77.5%). Moreover, combination of several biomarkers improved the sensitivity and specificity of the detection of patient response to over 97%. The 28 kDa protein was characterised as apolipoprotein A-I and the 7.77 kDa biomarker was identified as platelet factor 4. CONCLUSIONS Six plasma biomarkers are characterised, enabling the detection of patient response to infliximab with high sensitivity and specificity. Apolipoprotein A-1 was predictive of a good response to infliximab, whereas platelet factor 4 was associated with non-responders.
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Affiliation(s)
- C Trocmé
- GREPI CNRS UMR 5525, INSERM IFR 130, Université J Fourier, Grenoble, France
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Liu W, Li X, Ding F, Li Y. Using SELDI-TOF MS to identify serum biomarkers of rheumatoid arthritis. Scand J Rheumatol 2008; 37:94-102. [PMID: 18415765 DOI: 10.1080/03009740701747152] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVES No satisfactory biomarkers are currently available to screen for rheumatoid arthritis (RA). We have developed and evaluated surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) for detection and analysis of multiple proteins for distinguishing individuals with RA from control individuals. METHODS A total of 156 serum samples from 90 RA patients, 30 patients with ankylosing spondylitis (AS), and 36 healthy individuals were examined by SELDI technology. Spectral data were analysed by the support vector machine (SVM) approach and potential biomarkers were chosen for system training and were used to construct a diagnostic model. RESULTS Pattern 1, consisting of four protein peaks with m/z values of 3899, 4594, 7566, and 13,842, distinguished RA from the healthy samples with sensitivity of 90.0% and a specificity of 91.7%. Pattern 2, consisting of m/z peaks 4287 and 6471, distinguished RA from AS with a sensitivity of 86.7% and a specificity of 85.0%. CONCLUSION The combination of SELDI-TOF MS and SVM could facilitate the discovery of better biomarkers for RA and also provide a useful tool for molecular diagnosis in the future.
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Affiliation(s)
- W Liu
- Department of Rheumatology, Shandong University Qilu Hospital, Jinan, P.R. China
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de Seny D, Fillet M, Ribbens C, Marée R, Meuwis MA, Lutteri L, Chapelle JP, Wehenkel L, Louis E, Merville MP, Malaise M. Monomeric Calgranulins Measured by SELDI-TOF Mass Spectrometry and Calprotectin Measured by ELISA as Biomarkers in Arthritis. Clin Chem 2008; 54:1066-75. [DOI: 10.1373/clinchem.2007.099549] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
AbstractBackground: SELDI-TOF mass spectrometry (MS) is a high-throughput proteomic approach with potential for identifying novel forms of serum biomarkers of arthritis.Methods: We used SELDI-TOF MS to analyze serum samples from patients with various forms of inflammatory arthritis. Several protein profiles were collected on different Bio-Rad Laboratories ProteinChip arrays (CM10 and IMAC-Cu2+) and were evaluated statistically to select potential biomarkers.Results: SELDI-TOF MS analyses identified several calgranulin proteins [S100A8 (calgranulin A), S100A9 (calgranulin B), S100A9*, and S100A12 (calgranulin C)], serum amyloid A (SAA), SAA des-Arg (SAA-R), and SAA des-Arg/des-Ser (SAA-RS) as biomarkers and confirmed the results with other techniques, such as western blotting, immunoprecipitation, and nano-LC-MS/MS. The S100 proteins were all able to significantly differentiate samples from patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA), and ankylosing spondylitis (AS) from those of patients with inflammatory bowel diseases used as an inflammatory control (IC) group, whereas the SAA, SAA-R, and SAA-RS proteins were not, with the exception of AS. The 4 S100 proteins were coproduced in all of the pathologies and were significantly correlated with the plasma calprotectin concentration; however, these S100 proteins were correlated with the SAA peak intensities only in the RA and IC patient groups. In RA, these S100 proteins (except for S100A12) were significantly correlated with the serum concentrations of C-reactive protein, matrix metalloproteinase 3, and anti–cyclic citrullinated peptide and with the Disease Activity Score (DAS28).Conclusions: The SELDI-TOF MS technology is a powerful approach for analyzing the status of monomeric, truncated, or posttranslationally modified forms of arthritis biomarkers, such as the S100A8, S100A9, S100A12, and SAA proteins. The fact that the SELDI-TOF MS data were correlated with results obtained with the classic calprotectin ELISA test supports the reliability of this new proteomic technique.
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Affiliation(s)
- Dominique de Seny
- Laboratory of Rheumatology, GIGA Research, CHU, University of Liège
| | - Marianne Fillet
- Laboratory of Clinical Chemistry, GIGA Research, University of Liège
| | - Clio Ribbens
- Laboratory of Rheumatology, GIGA Research, CHU, University of Liège
| | | | | | - Laurence Lutteri
- Laboratory of Clinical Chemistry, GIGA Research, University of Liège
| | | | - Louis Wehenkel
- Bioinformatics and Modeling Unit, Department of Electrical Engineering & Computer Science, GIGA Research, University of Liège
| | - Edouard Louis
- Laboratory of Hepato-Gastroenterology, CHU, University of Liège, Liège, Belgium
| | | | - Michel Malaise
- Laboratory of Rheumatology, GIGA Research, CHU, University of Liège
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Gagnon A, Shi Q, Ye B. Surface-enhanced laser desorption/ionization mass spectrometry for protein and Peptide profiling of body fluids. Methods Mol Biol 2008; 441:41-56. [PMID: 18370310 DOI: 10.1007/978-1-60327-047-2_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Recently, Ciphergen Biosystems (Fremont, CA, USA) has developed a technique called surface-enhanced laser desorption/ionization (SELDI). This technology is based on ProteinChips(R) with chemically or biochemically modified surfaces for the selective retention and enrichment of protein subsets from a complex protein mixture. The proteins or peptides of interest can then be identified by using mass spectrometry (SELDI-MS). This highly sensitive and high-throughput technique can detect minute differences in proteins and peptide profiles between biological samples. The versatility of this technology enables a wide variety of applications in basic research, clinical, proteomic, and drug discovery such as identification of novel biomarkers associated with certain diseases or treatments. Many disease biomarkers or biomarker patterns have been identified using SELDI-MS in various laboratories. In this chapter, we provide a general guide to the profiling of proteins or peptides as well as biomarker discovery using the most common body fluids such as serum/plasma, nipple aspiration fluid, and urine.
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Affiliation(s)
- Audrey Gagnon
- Laboratory of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Dana-Farber Cancer Center, Boston, MA, USA
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63
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Meuwis MA, Fillet M, Lutteri L, Marée R, Geurts P, de Seny D, Malaise M, Chapelle JP, Wehenkel L, Belaiche J, Merville MP, Louis E. Proteomics for prediction and characterization of response to infliximab in Crohn's disease: a pilot study. Clin Biochem 2008; 41:960-7. [PMID: 18489908 DOI: 10.1016/j.clinbiochem.2008.04.021] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 04/07/2008] [Accepted: 04/19/2008] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Infliximab is the first anti-TNFalpha accepted by the Food and Drug Administration for use in inflammatory bowel disease treatment. Few clinical, biological and genetic factors tend to predict response in Crohn's disease (CD) patient subcategories, none widely predicting response to infliximab. DESIGN AND METHODS Twenty CD patients showing clinical response or non response to infliximab were used for serum proteomic profiling on Surface Enhanced Lazer Desorption Ionisation-Time of Flight-Mass Spectrometry (SELDI-TOF-MS), each before and after treatment. Univariate and multivariate data analysis were performed for prediction and characterization of response to infliximab. RESULTS We obtained a model of classification predicting response to treatment and selected relevant potential biomarkers, among which platelet aggregation factor 4 (PF4). We quantified PF4, sCD40L and IL-6 by ELISA for correlation studies. CONCLUSIONS This first proteomic pilot study on response to infliximab in CD suggests association between platelet metabolism and response to infliximab and requires validation studies on a larger cohort of patients.
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Affiliation(s)
- Marie-Alice Meuwis
- Laboratory of Clinical Chemistry, GIGA Research, University of Liège, Belgium
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Lambrecht S, Tilleman K, Elewaut D, Deforce D. Proteomics in rheumatology: The beginning of a fairy tale? Proteomics Clin Appl 2008; 2:411-9. [DOI: 10.1002/prca.200780084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Indexed: 11/11/2022]
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65
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Wilson R, Bateman JF. Cartilage proteomics: Challenges, solutions and recent advances. Proteomics Clin Appl 2008; 2:251-63. [DOI: 10.1002/prca.200780007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Hu CJ, Li YZ, Zhao GF, Li N, Xu Y, Tong DW, Zhang SL. Screening for specific biomarkers in serum for diagnosis of primary biliary cirrhosis using proteomic fingerprint technology. Shijie Huaren Xiaohua Zazhi 2008; 16:277-283. [DOI: 10.11569/wcjd.v16.i3.277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To screen for the potential protein biomarkers in serum for the diagnosis of primary biliary cirrhosis (PBC) using proteomic fingerprint technology.
METHODS: Proteomic fingerprint technology combining magnetic beads with MALDI-TOF-MS was used to profile and compare the serum proteins from 44 patients with PBC, 32 patients with other hepatic diseases and 43 healthy blood donors. Proteomic patterns associated with PBC were identified by Biomarker Patterns Software. Model of biomarkers was constructed and evaluated using the Biomarker Patterns Software.
RESULTS: A total of 69 discriminating m/z peaks were identified that were related to PBC (P < 0.05). The model of biomarkers constructed by the Biomarker Patterns Software based on the four biomarkers (3445, 4260, 8133 and 16290) generated excellent separation between the PBC and control groups. The sensitivity was 93.3% and the specificity was 95.1%. Blind test data indicated a sensitivity of 92.9% and a specificity of 82.4%.
CONCLUSION: Biomarkers for PBC can be discovered in serum by MALDI-TOF-MS combining the use of magnetic beads. The pattern of combined markers provides a powerful and reliable diagnostic method for PBC with a high sensitivity and specificity.
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Giusti L, Baldini C, Bazzichi L, Bombardieri S, Lucacchini A. Proteomic diagnosis of Sjögren's syndrome. Expert Rev Proteomics 2008; 4:757-67. [PMID: 18067414 DOI: 10.1586/14789450.4.6.757] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In the last few years, a growing interest has arisen in the application of proteomic analysis to rheumatic disease. Sjögren's syndrome is a systemic disease that affects exocrine glands directly, and is therefore expected to influence the composition of the whole human saliva and lachrymal fluid. Therefore, a rising number of studies have been performed in an attempt to characterize the salivary and lachrymal protein profiles of patients with Sjögren's syndrome by using a proteomic approach. This review summarizes the state of the art and the potential application of proteomics in the systematic search for diagnostic biomarkers in Sjögren's syndrome.
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Affiliation(s)
- Laura Giusti
- University of Pisa, Department of Psychiatry, Neurobiology, Pharmacology & Biotechnology, Via Bonanno 6, 56126 Pisa, Italy.
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Walker EJ, Siminovitch KA. Primer: genomic and proteomic tools for the molecular dissection of disease. ACTA ACUST UNITED AC 2007; 3:580-9. [PMID: 17906613 DOI: 10.1038/ncprheum0595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 06/05/2007] [Indexed: 12/29/2022]
Abstract
Completion of the Human Genome Project has been rapidly followed by the emergence of high-throughput technologies that combine automation, miniaturization, and many other strategies and tools to enable systematic surveys of genome composition and gene expression. Of particular relevance to the prevention and management of disease are technologies such as high-throughput DNA genotyping, microarray-based gene-expression profiling, and mass spectrometry-facilitated protein profiling--platforms that collectively support the comprehensive analysis of DNA sequence variants across the genome and the global gene and protein expression changes that distinguish health from disease. Now used extensively in all facets of biomedical investigation, genomic and proteomic tools are already beginning to pinpoint molecular variants that influence risk and outcome in common diseases, and to thereby inform and direct development of novel molecular biomarkers and drug targets. As evidenced by recent advances in DNA sequencing methods, continued improvements in the scope, power, and cost efficiency of genomic and proteomic technologies should ensure their capacity to provide the scale and depth of knowledge required for translating genome sequence information into major medical impact.
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69
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Lee JH, Roh MR, Bang D, Lee KH. Using proteomics to identify targets of antiendothelial cell antibodies. Expert Rev Clin Immunol 2007; 3:983-91. [PMID: 20477145 DOI: 10.1586/1744666x.3.6.983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antiendothelial cell antibodies represent a heterogeneous group of antibodies directed against a variety of antigen determinants of endothelial cells. Antibodies reacting with endothelial structures have been detected in sera from patients with autoimmune vasculitis, both primary and secondary to systemic connective tissue diseases. It may interfere with several functions and, therefore, may be a pathophysiological relevance. The analysis of the antigens recognized by antiendothelial cell antibodies showed that the antibodies are directed against a heterogeneous family of both constitutive and nonconstitutive surface endothelial proteins. Proteomics is a field of science that evaluates a large number of proteins expressed from a given cell line or organism. The technology of proteomics has been used as a method for discovering the target protein specific to a particular disease by searching for the expression or modification of the protein. Recently, progress has been made in defining the target antigens of these antibodies and proteomic technologies is one of them. This review will focus on the proteomic technologies in searching autoantigens/autoantibodies associated with disease of the endothelium.
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Affiliation(s)
- Ju Hee Lee
- Yonsei University College of Medicine, Department of Dermatology and Cutaneous Biology Research Institute, 134 Shinchon-Dong, Seodaemoon-Gu, Seoul 120-752, Korea.
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Naishiro Y, Suzuki C, Kimura M, Yamamoto M, Takahashi H, Sohma H, Hori T, Shinomura Y, Kokai Y, Imai K. [Plasma analysis of rheumatoid arthritis by SELDI]. ACTA ACUST UNITED AC 2007; 30:145-50. [PMID: 17603254 DOI: 10.2177/jsci.30.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To identify protein biomarkers linking to disease activity and treatment responses of patients with rheumatoid arthritis (RA), proteomic study using mass spectrometric analysis of plasma proteins was performed. Proteomic profiling technologies can simultaneously resolve and analyze multiple proteins in plasma. Evaluation of multiple proteins of the plasma will be essential to discover protein biomarkers. In this study, we used protein chip surface enhanced laser desorption/ionization time of flight mass spectrometry approach (SELDI-TOF MS). Through differential profiling of plasma proteins, we selected two prospective candidate biomarkers. One mass spectrometric peak distinguished patients with RA from healthy controls was transthyretin (TTR) and the other distinguished inactive patients with RA from patients with active RA was Serum Amyloid A (SAA). This study demonstrates that proteomic profiling using mass spectrometry of plasma greatly facilitates global discovery and verify clinically relevant sets of disease biomarker directly links to disease activity and treatment responses.
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Affiliation(s)
- Yasuyoshi Naishiro
- Department of Biomedical Engineering, Sapporo Medical University School of Medicine
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71
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Bons JAP, van Dieijen-Visser MP, Wodzig WKWH. Clinical proteomics in chronic inflammatory diseases: A review. Proteomics Clin Appl 2007; 1:1123-33. [DOI: 10.1002/prca.200700067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Indexed: 11/10/2022]
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72
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Wada-Isoe K, Michio K, Imamura K, Nakaso K, Kusumi M, Kowa H, Nakashima K. Serum proteomic profiling of dementia with Lewy bodies: diagnostic potential of SELDI-TOF MS analysis. J Neural Transm (Vienna) 2007; 114:1579-83. [PMID: 17690946 DOI: 10.1007/s00702-007-0794-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 07/19/2007] [Indexed: 10/23/2022]
Abstract
Dementia with Lewy bodies (DLB) is the second most common senile degenerative dementia after Alzheimer's disease (AD). The presentation of overlapping symptoms between these two disorders leads to difficulties in the determination of clinical entities. Serum samples were subjected to surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) analysis in order to identify a diagnostic marker for DLB. Four putative protein peaks (m/z 3,883, 4,964, 7,761 and 10,534) were differentially expressed in DLB patients compared to AD patients and control subjects. Receiver operating characteristics (ROC) analysis of a multivariate logistic model of the combination of three peaks (m/z 3,883, 7,761 and 10,534) exhibited the highest discriminatory ability of DLB subjects from non-DLB subjects with a sensitivity of 83.3%, a specificity of 95.8%, a positive predictive value of 90.9% and a negative predictive value of 92.0%. SELDI-TOF MS profiling, therefore, has revealed a serum signature with high diagnostic potential for DLB.
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Affiliation(s)
- K Wada-Isoe
- Department of Neurology, Faculty of Medicine, Institute of Neurological Sciences, Tottori University, Yonago, Japan.
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73
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Luque-Garcia JL, Neubert TA. Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry. J Chromatogr A 2007; 1153:259-76. [PMID: 17166507 PMCID: PMC7094463 DOI: 10.1016/j.chroma.2006.11.054] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/06/2006] [Accepted: 11/16/2006] [Indexed: 01/14/2023]
Abstract
In this article, we present an overview of the different strategies for sample preparation for identification by mass spectrometry (MS) of biomarkers from serum and/or plasma. We consider the effects of the variables involved in sample collection, handling and storage, and describe different approaches for removal of high abundance proteins and serum/plasma fractionation. We review the advantages and disadvantages of such techniques as centrifugal ultrafiltration, different formats for solid phase extraction, organic solvent extraction, gel and capillary electrophoresis, and liquid chromatography. We also discuss a variety of current proteomic methods and their main applications for biomarker-related studies.
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Affiliation(s)
| | - Thomas A. Neubert
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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74
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Villar-Garea A, Griese M, Imhof A. Biomarker discovery from body fluids using mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:105-14. [PMID: 17097359 DOI: 10.1016/j.jchromb.2006.09.017] [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] [Received: 06/24/2006] [Revised: 08/22/2006] [Accepted: 09/08/2006] [Indexed: 11/18/2022]
Abstract
Systems analysis of body fluids by mass spectrometry (MS) is an upcoming field of biomarker research. This approach is extremely attractive because it does not require biomarker candidates and the sample preparation is simple. However, during the development of the technique strong critical comments were made on the poor reproducibility, the special characteristics of blood as a source of peptides and on the frequent non-adequate statistical analysis of the data. Here we discuss the efforts made in the last few years to develop suitable protocols, which could lead to biomarker discovery from body fluids by mass spectrometry. Our review focuses on the systems analysis of non-digested blood serum or plasma samples by MALDI-TOF and SELDI-TOF.
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Affiliation(s)
- Ana Villar-Garea
- Histone modifications group, Adolf-Butenandt Institute, Ludwig-Maximilians University of Munich, Schillerstr 44, 80336 Munich, Germany
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75
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Li Y, Lee HJ, Corn RM. Detection of protein biomarkers using RNA aptamer microarrays and enzymatically amplified surface plasmon resonance imaging. Anal Chem 2007; 79:1082-8. [PMID: 17263339 PMCID: PMC2515860 DOI: 10.1021/ac061849m] [Citation(s) in RCA: 229] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A methodology for the detection of protein biomarkers at picomolar concentrations that utilizes surface plasmon resonance imaging (SPRI) measurements of RNA aptamer microarrays is developed. The adsorption of proteins onto the RNA microarray is detected by the formation of a surface aptamer-protein-antibody complex. The SPRI response signal is then amplified using a localized precipitation reaction catalyzed by the enzyme horseradish peroxidase that is conjugated to the antibody. This enzymatically amplified SPRI methodology is first characterized by the detection of human thrombin at a concentration of 500 fM; the appropriate thrombin aptamer for the sandwich assay is identified from a microarray of three potential thrombin aptamer candidates. The SPRI method is then used to detect the protein vascular endothelial growth factor (VEGF) at a biologically relevant concentration of 1 pM. VEGF is a signaling protein that has been used as a serum biomarker for rheumatoid arthritis, breast cancer, lung cancer, and colorectal cancer and is also associated with age-related macular degeneration.
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76
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Benninghoff AD. Toxicoproteomics--the next step in the evolution of environmental biomarkers. Toxicol Sci 2007; 95:1-4. [PMID: 17209232 DOI: 10.1093/toxsci/kfl157] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Abby D Benninghoff
- Department of Environmental and Molecular Toxicology, Oregon State University, 1007 Agricultural and Life Sciences Building, Corvallis, Oregon 97331, USA.
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77
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Abstract
Autoimmune diseases are common by diseases characterized by disorders of immune responses and autoimmune impairment involving multiple tissues, organs and systems. The autoantigens (Ags)/autoantibodies (Abs) are not only hallmarks but also involved in pathogenesis of autoimmune diseases. In recent years, proteomics technologies have been used and demonstrated effective in searching new Ags/Abs as well as disease biomarkers in autoimmune diseases.
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Affiliation(s)
- Y Xiang
- Department of Bioregulation and Proteomics, Institute of Medical Science, St Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
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78
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Hui L, Diandong H, Baoxia Z, Da W, Hong Y, Xiaoyi W. Serum proteomic profiling associated with immune system impaired by stress using ProteinChip technology. Neuroimmunomodulation 2007; 14:326-30. [PMID: 18421221 DOI: 10.1159/000126921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 02/28/2008] [Indexed: 12/28/2022] Open
Abstract
We set out to use proteomic profiling as a means of defining serum peptides that are indicative of a stress response related to an impact on the immune system. Two types of mouse models with the immune response impaired under stress (restraint stress and thermal stress) comprised the stressed groups (n = 10 in each group), while mice without stress represented the control group (n = 10). ProteinChip technology (surface-enhanced laser desorption/ionization time-of-flight mass spectrometry) was used to investigate the serum proteomic profiles. Histopathological examination of spleens from the stressed and control groups was performed to select appropriate individuals. Compared with the spleens of normal mice, those of mice subjected to restraint and thermal stress had decreased white pulp and lymphoid nodules, and their distribution and structure changed irregularly. Pathological changes occurred in all individuals in both stressed groups. The m/z values of the protein peaks ranged from 1,500 to 50,000 daltons and were mainly in the 2,000- to 20,000-dalton range. One hundred and fifty protein peaks were detected in the three groups. Four downregulated universal stress protein peaks with m/z of 4,389, 5,341, 5,526, and 6,252 were finally selected. Unexpectedly, no upregulated universal stress protein peaks were detected. These results suggested that impairment of the immune system results from inhibition of growth-promoting factors associated with the immune system. Identified protein peaks may be biomarkers of the impaired immune system under stress.
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Affiliation(s)
- Liu Hui
- College of Medical Laboratory, Dalian Medical University, Dalian, China.
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79
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Meuwis MA, Fillet M, Geurts P, de Seny D, Lutteri L, Chapelle JP, Bours V, Wehenkel L, Belaiche J, Malaise M, Louis E, Merville MP. Biomarker discovery for inflammatory bowel disease, using proteomic serum profiling. Biochem Pharmacol 2006; 73:1422-33. [PMID: 17258689 DOI: 10.1016/j.bcp.2006.12.019] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Revised: 12/15/2006] [Accepted: 12/15/2006] [Indexed: 02/07/2023]
Abstract
Crohn's disease and ulcerative colitis known as inflammatory bowel diseases (IBD) are chronic immuno-inflammatory pathologies of the gastrointestinal tract. These diseases are multifactorial, polygenic and of unknown etiology. Clinical presentation is non-specific and diagnosis is based on clinical, endoscopic, radiological and histological criteria. Novel markers are needed to improve early diagnosis and classification of these pathologies. We performed a study with 120 serum samples collected from patients classified in 4 groups (30 Crohn, 30 ulcerative colitis, 30 inflammatory controls and 30 healthy controls) according to accredited criteria. We compared protein sera profiles obtained with a Surface Enhanced Laser Desorption Ionization-Time of Flight-Mass Spectrometer (SELDI-TOF-MS). Data analysis with univariate process and a multivariate statistical method based on multiple decision trees algorithms allowed us to select some potential biomarkers. Four of them were identified by mass spectrometry and antibody based methods. Multivariate analysis generated models that could classify samples with good sensitivity and specificity (minimum 80%) discriminating groups of patients. This analysis was used as a tool to classify peaks according to differences in level on spectra through the four categories of patients. Four biomarkers showing important diagnostic value were purified, identified (PF4, MRP8, FIBA and Hpalpha2) and two of these: PF4 and Hpalpha2 were detected in sera by classical methods. SELDI-TOF-MS technology and use of the multiple decision trees method led to protein biomarker patterns analysis and allowed the selection of potential individual biomarkers. Their downstream identification may reveal to be helpful for IBD classification and etiology understanding.
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Affiliation(s)
- Marie-Alice Meuwis
- Laboratory of Clinical Chemistry, GIGA Research, CHU, University of Liège, B34, 4000 Liège, Belgium
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80
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Abstract
The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.
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Affiliation(s)
- Shen Hu
- School of Dentistry, Division of Oral Biology and Medicine, Dental Research Institute, University of California, Los Angeles, CA 90095, USA.
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81
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Lambrecht S, Deforce D, Elewaut D. Entering the era of proteomics in rheumatology. Expert Opin Drug Discov 2006; 1:539-48. [DOI: 10.1517/17460441.1.6.539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stijn Lambrecht
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University Hospital, Harelbekestraat 72, 9000, Ghent, Belgium
| | - Dirk Elewaut
- Laboratory for Molecular Immunology and Inflammation, Division of Rheumatology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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82
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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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