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Nimer RM, Abdel Rahman AM. Recent advances in proteomic-based diagnostics of cystic fibrosis. Expert Rev Proteomics 2023; 20:151-169. [PMID: 37766616 DOI: 10.1080/14789450.2023.2258282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 07/06/2023] [Indexed: 09/29/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF. AREAS COVERED We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers. EXPERT OPINION Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas M Abdel Rahman
- Metabolomics Section, Department of Clinical Genomics, Center for Genome Medicine, King Faisal Specialist Hospital and Research Centre (KFSHRC), Riyadh, Saudi Arabia
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Milinic T, McElvaney OJ, Goss CH. Diagnosis and Management of Cystic Fibrosis Exacerbations. Semin Respir Crit Care Med 2023; 44:225-241. [PMID: 36746183 PMCID: PMC10131792 DOI: 10.1055/s-0042-1760250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
With the improving survival of cystic fibrosis (CF) patients and the advent of highly effective cystic fibrosis transmembrane conductance regulator (CFTR) therapy, the clinical spectrum of this complex multisystem disease continues to evolve. One of the most important clinical events for patients with CF in the course of this disease is acute pulmonary exacerbation (PEx). Clinical and microbial epidemiology studies of CF PEx continue to provide important insight into the disease course, prognosis, and complications. This work has now led to several large-scale clinical trials designed to clarify the treatment paradigm for CF PEx. The primary goal of this review is to provide a summary and update of the pathophysiology, clinical and microbial epidemiology, outcome and treatment of CF PEx, biomarkers for exacerbation, and the impact of highly effective modulator therapy on these events moving forward.
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Affiliation(s)
- Tijana Milinic
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Oliver J McElvaney
- Cysic Fibrosis Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington
| | - Christopher H Goss
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington
- Cysic Fibrosis Therapeutics Development Network Coordinating Center, Seattle Children's Research Institute, Seattle, Washington
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
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D’Amato M, Iadarola P, Viglio S. Proteomic Analysis of Human Sputum for the Diagnosis of Lung Disorders: Where Are We Today? Int J Mol Sci 2022; 23:ijms23105692. [PMID: 35628501 PMCID: PMC9144372 DOI: 10.3390/ijms23105692] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
The identification of markers of inflammatory activity at the early stages of pulmonary diseases which share common characteristics that prevent their clear differentiation is of great significance to avoid misdiagnosis, and to understand the intrinsic molecular mechanism of the disorder. The combination of electrophoretic/chromatographic methods with mass spectrometry is currently a promising approach for the identification of candidate biomarkers of a disease. Since the fluid phase of sputum is a rich source of proteins which could provide an early diagnosis of specific lung disorders, it is frequently used in these studies. This report focuses on the state-of-the-art of the application, over the last ten years (2011-2021), of sputum proteomics in the investigation of severe lung disorders such as COPD; asthma; cystic fibrosis; lung cancer and those caused by COVID-19 infection. Analysis of the complete set of proteins found in sputum of patients affected by these disorders has allowed the identification of proteins whose levels change in response to the organism's condition. Understanding proteome dynamism may help in associating these proteins with alterations in the physiology or progression of diseases investigated.
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Affiliation(s)
- Maura D’Amato
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
| | - Paolo Iadarola
- Department of Biology and Biotechnologies “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
- Correspondence:
| | - Simona Viglio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
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Challenges in Serologic Diagnostics of Neglected Human Systemic Mycoses: An Overview on Characterization of New Targets. Pathogens 2022; 11:pathogens11050569. [PMID: 35631090 PMCID: PMC9143782 DOI: 10.3390/pathogens11050569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 12/04/2022] Open
Abstract
Systemic mycoses have been viewed as neglected diseases and they are responsible for deaths and disabilities around the world. Rapid, low-cost, simple, highly-specific and sensitive diagnostic tests are critical components of patient care, disease control and active surveillance. However, the diagnosis of fungal infections represents a great challenge because of the decline in the expertise needed for identifying fungi, and a reduced number of instruments and assays specific to fungal identification. Unfortunately, time of diagnosis is one of the most important risk factors for mortality rates from many of the systemic mycoses. In addition, phenotypic and biochemical identification methods are often time-consuming, which has created an increasing demand for new methods of fungal identification. In this review, we discuss the current context of the diagnosis of the main systemic mycoses and propose alternative approaches for the identification of new targets for fungal pathogens, which can help in the development of new diagnostic tests.
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Woodall M, Reidel B, Kesimer M, Tarran R, Baines DL. Culture with apically applied healthy or disease sputum alters the airway surface liquid proteome and ion transport across human bronchial epithelial cells. Am J Physiol Cell Physiol 2021; 321:C954-C963. [PMID: 34613844 PMCID: PMC8714986 DOI: 10.1152/ajpcell.00234.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Airway secretions contain many signaling molecules and peptides/proteins that are
not found in airway surface liquid (ASL) generated by normal human bronchial
epithelial cells (NHBEs) in vitro. These play a key role in innate defense and
mediate communication between the epithelium, the immune cells, and the external
environment. We investigated how culture of NHBE with apically applied
secretions from healthy or diseased (cystic fibrosis, CF) lungs affected
epithelial function with a view to providing better in vitro models of the in
vivo environment. NHBEs from 6 to 8 different donors were cultured at air-liquid
interface (ALI), with apically applied sputum from normal healthy donors (normal
lung sputum; NLS) or CF donors (CFS) for 2–4 h, 48 h, or with sputum
reapplied over 48 h. Proteomics analysis was carried out on the sputa and on the
NHBE ASL before and after culture with sputa. Transepithelial electrical
resistance (TEER), short circuit current (Isc), and changes to ASL
height were measured. There were 71 proteins common to both sputa but not ASL.
The protease:protease inhibitor balance was increased in CFS compared with NLS
and ASL. Culture of NHBE with sputa for 48 h identified additional factors not
present in NLS, CFS, or ASL alone. Culture with either NLS or CFS for 48 h
increased cystic fibrosis transmembrane regulator (CFTR) activity,
calcium-activated chloride channel (CaCC) activity, and changed ASL height.
These data indicate that culture with healthy or disease sputum changes the
proteomic profile of ASL and ion transport properties of NHBE and this may
increase physiological relevance when using in vitro airway models.
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Affiliation(s)
- Maximillian Woodall
- Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, Tooting, London, United Kingdom
| | - Boris Reidel
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mehmet Kesimer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Robert Tarran
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Deborah L Baines
- Institute for Infection and Immunity, St George's, University of London, Cranmer Terrace, Tooting, London, United Kingdom
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Mass Spectrometry-Based Proteomic and Immunoproteomic Analyses of the Candida albicans Hyphal Secretome Reveal Diagnostic Biomarker Candidates for Invasive Candidiasis. J Fungi (Basel) 2021; 7:jof7070501. [PMID: 34201883 PMCID: PMC8306665 DOI: 10.3390/jof7070501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/18/2021] [Indexed: 01/08/2023] Open
Abstract
Invasive candidiasis (IC) is associated with high morbidity and mortality in hospitalized patients if not diagnosed early. Long-term use of central venous catheters is a predisposing factor for IC. Hyphal forms of Candida albicans (the major etiological agent of IC) are related to invasion of host tissues. The secreted proteins of hyphae are involved in virulence, host interaction, immune response, and immune evasion. To identify IC diagnostic biomarker candidates, we characterized the C. albicans hyphal secretome by gel-free proteomic analysis, and further assessed the antibody-reactivity patterns to this subproteome in serum pools from 12 patients with non-catheter-associated IC (ncIC), 11 patients with catheter-associated IC (cIC), and 11 non-IC patients. We identified 301 secreted hyphal proteins stratified to stem from the extracellular region, cell wall, cell surface, or intracellular compartments. ncIC and cIC patients had higher antibody levels to the hyphal secretome than non-IC patients. Seven secreted hyphal proteins were identified to be immunogenic (Bgl2, Eno1, Pgk1, Glx3, Sap5, Pra1 and Tdh3). Antibody-reactivity patterns to Bgl2, Eno1, Pgk1 and Glx3 discriminated IC patients from non-IC patients, while those to Sap5, Pra1 and Tdh3 differentiated between cIC and non-IC patients. These proteins may be useful for development of future IC diagnostic tests.
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Tanaka K, Enomoto N, Hozumi H, Isayama T, Naoi H, Aono Y, Katsumata M, Yasui H, Karayama M, Suzuki Y, Furuhashi K, Fujisawa T, Inui N, Nakamura Y, Suda T. Serum S100A8 and S100A9 as prognostic biomarkers in acute exacerbation of idiopathic pulmonary fibrosis. Respir Investig 2021; 59:827-836. [PMID: 34154976 DOI: 10.1016/j.resinv.2021.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/16/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) is a devastating and life-threatening condition during its clinical course. Biomarkers for precisely anticipating the prognosis of AE-IPF remain to be fully established. The objective of this study was to clarify whether S100A8 and S100A9, which are calcium-binding proteins mainly produced by activated neutrophils, are significant prognostic biomarkers in AE-IPF. METHODS Thirty-seven patients with AE-IPF who were diagnosed and treated at our hospital were retrospectively evaluated. The serum levels of S100A8 and S100A9 were measured using enzyme-linked immunosorbent assay, and the relationships between these levels and clinical parameters or prognosis were evaluated. RESULTS The serum levels of S100A8 (median 386.5 ng/mL) and S100A9 (median 60.2 ng/mL) in patients with AE-IPF were significantly higher than those in age-matched healthy controls and in patients at IPF diagnosis (p < 0.001 for all combinations). The serum levels of S100A8 negatively correlated with percent forced vital capacity (r = -0.356, p = 0.049) and positively correlated with peripheral white blood cell number (r = 0.509, p = 0.002). Immunohistochemical staining of autopsy lung specimens showed that neutrophils, present mainly in the alveolar septum, were positive for S100A8 and S100A9. Patients with AE-IPF with higher levels of S100A8 or S100A9 showed significantly worse 3-month survival than those with lower levels (log-rank test, both p = 0.028). Finally, in multivariate analysis, the serum levels of both S100A8 and S100A9 were significant prognostic factors (hazard ratio 4.032, p = 0.023 and hazard ratio 4.327, p = 0.012). CONCLUSION The serum levels of S100A8 and S100A9 at AE were significant prognostic biomarkers in patients with AE-IPF.
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Affiliation(s)
- Kazuki Tanaka
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriyuki Enomoto
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan; Health Administration Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Hironao Hozumi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takuya Isayama
- Medical & Biological Laboratories Co., Ltd., Nagoya, Japan
| | - Hyogo Naoi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuya Aono
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mineo Katsumata
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideki Yasui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Karayama
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuzo Suzuki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuki Furuhashi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoyuki Fujisawa
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naoki Inui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan; Department of Clinical Pharmacology and Therapeutics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yutaro Nakamura
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
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Immunoproteomic analysis of Clostridium botulinum type B secretome for identification of immunogenic proteins against botulism. Biotechnol Lett 2021; 43:1019-1036. [PMID: 33629143 PMCID: PMC7904509 DOI: 10.1007/s10529-021-03091-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 02/01/2021] [Indexed: 11/12/2022]
Abstract
Objectives To identify immunogenic proteins of C. botulinum type B secretome by immunoproteomic analysis. Results In the present study, an attempt was made to elucidate the vaccine candidates/diagnostic molecules against botulism using immuno proteomic approach. C. botulinum type B secretome was elucidated when it was grown in TPGY as well as CMM media. Predominant 51 proteins were identified in both the media using 2-DE and mass spectrometry analysis. 2D gels (CMM & TPGY) were probed with respected proteins mice antiserum and obtained 17 and 10 immunogenic proteins in TPGY as well as CMM media respectively. Hypothetical protein CLOSPO_00563, ornithine carbamoyl transferase, FlaA, molecular chaperone GroEL and secreted protease proteins were found as the common immuno dominant proteins in both media. Polyclonal Antibodies raised against C. botulinum types A and E showed cross-reactivity with secretome C. botulinum type B at the lowest dilution (1:1000) but did not show cross reactivity with highest dilution (1:30,000) with C. botulinum type B secretome. Polyclonal antibodies against C. botulinum type F secretome did not show cross reactivity with C. botulinum type B secretome. Conclusions Identified immunogenic proteins can be used as vaccine candidates and diagnostic markers for the infant and wound botulism but common immunogenic proteins may be the best vaccine candidate molecule for development of vaccine as well as diagnostic system against the infant and wound botulism. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-021-03091-4.
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Wei L, Wang Y, Lin L, Zhang L, Shi Y, Xiang P, Cao S, Shen M, Yang P. Identification of potential serum biomarkers of acute paraquat poisoning in humans using an iTRAQ quantitative proteomic. RSC Adv 2018; 8:10598-10609. [PMID: 35540476 PMCID: PMC9078879 DOI: 10.1039/c7ra12956d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/28/2019] [Accepted: 03/07/2018] [Indexed: 12/18/2022] Open
Abstract
Paraquat (PQ) poisoning has high mortality rates in many countries. Due to it readily being absorbed through the gastrointestinal tract and rapidly excreted in the urine, few biomarkers possess satisfactory specificity and sensitivity in diagnostic and forensic practices. To investigate serum biomarkers in patients with PQ poisoning, pooled sera was analyzed using a proteomic approach based on iTRAQ coupled LC-MS/MS. Of the 413 proteins identified with high confidence, 81 were found to be differentially expressed (1.5-fold change) in the sera of patients with PQ poisoning. The differential expression pattern of 4 of these proteins was validated by enzyme-linked immunosorbent assay (ELISA) in clinical samples. A sera sample from a PQ poisoning patient has shown relatively increased abundance of S100A8 and S100A9. The overexpression of S100A8 and S100A9 was further validated in the lung tissue of PQ-treated rat associated with lung damage. Meanwhile, we identified another two down-expressed proteins, transferrin receptor protein 1 (TfR1) and serum amyloid P-component (SAP), which may be also practicable in human clinical samples as PQ poisoning serum biomarkers. Furthermore, receiver operating characteristic curve analysis confirmed that the expression levels of S100 alarmins, TfR1 and SAP in patient serum could provide a discriminatory diagnostic test for predicting PQ poisoning in patients. Therefore, our results suggest that increased serum levels of S100 alarmins and decreased serum levels of TfR1 and SAP may constitute potential biomarkers for the prediction of PQ poisoning in humans, and might be novel therapeutic targets in PQ poisoning.
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Affiliation(s)
- Liming Wei
- Institutes of Biomedical Sciences & Department of Chemistry, Fudan University Shanghai China
- Shanghai Songjiang District Central Hospital Shanghai China
| | - Yi Wang
- Institutes of Biomedical Sciences & Department of Chemistry, Fudan University Shanghai China
| | - Ling Lin
- Institutes of Biomedical Sciences & Department of Chemistry, Fudan University Shanghai China
| | - Lei Zhang
- Institutes of Biomedical Sciences & Department of Chemistry, Fudan University Shanghai China
| | - Yan Shi
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Science, Ministry of Justice Shanghai China
| | - Ping Xiang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Science, Ministry of Justice Shanghai China
| | - Shujun Cao
- Shanghai Songjiang District Central Hospital Shanghai China
| | - Min Shen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Institute of Forensic Science, Ministry of Justice Shanghai China
| | - Pengyuan Yang
- Institutes of Biomedical Sciences & Department of Chemistry, Fudan University Shanghai China
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Talwar H, Hanoudi SN, Geamanu A, Kissner D, Draghici S, Samavati L. Detection of Cystic Fibrosis Serological Biomarkers Using a T7 Phage Display Library. Sci Rep 2017; 7:17745. [PMID: 29255267 PMCID: PMC5735098 DOI: 10.1038/s41598-017-18041-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 11/19/2017] [Indexed: 12/02/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder affecting the cystic fibrosis transmembrane conductance regulator (CFTR). CF is characterized by repeated lung infections leading to respiratory failure. Using a high-throughput method, we developed a T7 phage display cDNA library derived from mRNA isolated from bronchoalveolar lavage (BAL) cells and leukocytes of sarcoidosis patients. This library was biopanned to obtain 1070 potential antigens. A microarray platform was constructed and immunoscreened with sera from healthy (n = 49), lung cancer (LC) (n = 31) and CF (n = 31) subjects. We built 1,000 naïve Bayes models on the training sets. We selected the top 20 frequently significant clones ranked with student t-test discriminating CF antigens from healthy controls and LC at a False Discovery Rate (FDR) < 0.01. The performances of the models were validated on an independent validation set. The mean of the area under the receiver operating characteristic (ROC) curve for the classifiers was 0.973 with a sensitivity of 0.999 and specificity of 0.959. Finally, we identified CF specific clones that correlate highly with sweat chloride test, BMI, and FEV1% predicted values. For the first time, we show that CF specific serological biomarkers can be identified through immunocreenings of a T7 phage display library with high accuracy, which may have utility in development of molecular therapy.
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Affiliation(s)
- Harvinder Talwar
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA
| | - Samer Najeeb Hanoudi
- Department of Computer Science, Wayne State University, 540 E, Canfield, Detroit, MI, 48201, USA
| | - Andreea Geamanu
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA
| | - Dana Kissner
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA
| | - Sorin Draghici
- Department of Computer Science, Wayne State University, 540 E, Canfield, Detroit, MI, 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, 540 E, Canfield, Detroit, MI, 48201, USA
| | - Lobelia Samavati
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University School of Medicine and Detroit Medical Center, Detroit, MI, 48201, USA. .,Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 E, Canfield, Detroit, MI, 48201, USA.
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Pattison SH, Gibson DS, Johnston E, Peacock S, Rivera K, Tunney MM, Pappin DJ, Elborn JS. Proteomic profile of cystic fibrosis sputum cells in adults chronically infected with Pseudomonas aeruginosa. Eur Respir J 2017; 50:50/1/1601569. [DOI: 10.1183/13993003.01569-2016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 03/29/2017] [Indexed: 12/11/2022]
Abstract
Lung disease is the main cause of morbidity and mortality in cystic fibrosis (CF), and involves chronic infection and perturbed immune responses. Tissue damage is mediated mostly by extracellular proteases, but other cellular proteins may also contribute to damage through their effect on cell activities and/or release into sputum fluid by means of active secretion or cell death.We employed MudPIT (multidimensional protein identification technology) to identify sputum cellular proteins with consistently altered abundance in adults with CF, chronically infected with Pseudomonas aeruginosa, compared with healthy controls. Ingenuity Pathway Analysis, Gene Ontology, protein abundance and correlation with lung function were used to infer their potential clinical significance.Differentially abundant proteins relate to Rho family small GTPase activity, immune cell movement/activation, generation of reactive oxygen species, and dysregulation of cell death and proliferation. Compositional breakdown identified high abundance of proteins previously associated with neutrophil extracellular traps. Furthermore, negative correlations with lung function were detected for 17 proteins, many of which have previously been associated with lung injury.These findings expand our current understanding of the mechanisms driving CF lung disease and identify sputum cellular proteins with potential for use as indicators of disease status/prognosis, stratification determinants for treatment prescription or therapeutic targets.
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12
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Kamath KS, Kumar SS, Kaur J, Venkatakrishnan V, Paulsen IT, Nevalainen H, Molloy MP. Proteomics of hosts and pathogens in cystic fibrosis. Proteomics Clin Appl 2015; 9:134-46. [DOI: 10.1002/prca.201400122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/27/2014] [Accepted: 11/18/2014] [Indexed: 12/13/2022]
Affiliation(s)
| | - Sheemal Shanista Kumar
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Jashanpreet Kaur
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | | | - Ian T. Paulsen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
| | - Mark P. Molloy
- Department of Chemistry and Biomolecular Sciences; Macquarie University; Sydney Australia
- Australian Proteome Analysis Facility; Macquarie University; Sydney Australia
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Jeanson L, Guerrera IC, Papon JF, Chhuon C, Zadigue P, Prulière-Escabasse V, Amselem S, Escudier E, Coste A, Edelman A. Proteomic analysis of nasal epithelial cells from cystic fibrosis patients. PLoS One 2014; 9:e108671. [PMID: 25268127 PMCID: PMC4182543 DOI: 10.1371/journal.pone.0108671] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/24/2014] [Indexed: 11/21/2022] Open
Abstract
The pathophysiology of cystic fibrosis (CF) lung disease remains incompletely understood. New explanations for the pathogenesis of CF lung disease may be discovered by studying the patterns of protein expression in cultured human nasal epithelial cells (HNEC). To that aim, we compared the level of protein expressions in primary cultures of HNEC from nasal polyps secondary to CF (CFNP, n = 4), primary nasal polyps (NP, n = 8) and control mucosa (CTRL, n = 4) using isobaric tag for relative and absolute quantification (iTRAQ) labeling coupled with liquid chromatography (LC)-MS-MS. The analysis of the data revealed 42 deregulated protein expressions in CFNP compared to NP and CTRL, suggesting that these alterations are related to CF. Overall, AmiGo analysis highlighted six major pathways important for cell functions that seem to be impaired: metabolism, G protein process, inflammation and oxidative stress response, protein folding, proteolysis and structural proteins. Among them, glucose and fatty acid metabolic pathways could be impaired in CF with nine deregulated proteins. Our proteomic study provides a reproducible set of differentially expressed proteins in airway epithelial cells from CF patients and reveals many novel deregulated proteins that could lead to further studies aiming to clarify the involvement of such proteins in CF pathophysiology.
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Affiliation(s)
- Ludovic Jeanson
- Service de Génétique et Embryologie Médicales, Unité Mixte de Recherche_Scientifique 933, Institut National de la Santé et de la Recherche Médicale, Université Pierre et Marie Curie – Paris 6, and Assistance Publique – Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
| | - Ida Chiara Guerrera
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
- Plateau Proteome Necker, Structure Fédérative de Recherche de Necker, Université Paris Descartes, Paris, France
| | - Jean-François Papon
- Unité Mixte de Recherche_Scientifique 855, Institut National de la Santé et de la Recherche Médicale, Université Paris 12, Faculté de Médecine, Créteil, France
- Service d’Otorhinolaryngologie et de chirurgie cervico-faciale, Assistance Publique – Hôpitaux de Paris, Hôpital inter-communal et Groupe Hospitalier Henri Mondor-Albert Chenevier, Créteil, France
| | - Cerina Chhuon
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
- Plateau Proteome Necker, Structure Fédérative de Recherche de Necker, Université Paris Descartes, Paris, France
| | - Patricia Zadigue
- Unité Mixte de Recherche_Scientifique 855, Institut National de la Santé et de la Recherche Médicale, Université Paris 12, Faculté de Médecine, Créteil, France
| | - Virginie Prulière-Escabasse
- Service d’Otorhinolaryngologie et de chirurgie cervico-faciale, Assistance Publique – Hôpitaux de Paris, Hôpital inter-communal et Groupe Hospitalier Henri Mondor-Albert Chenevier, Créteil, France
| | - Serge Amselem
- Service de Génétique et Embryologie Médicales, Unité Mixte de Recherche_Scientifique 933, Institut National de la Santé et de la Recherche Médicale, Université Pierre et Marie Curie – Paris 6, and Assistance Publique – Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - Estelle Escudier
- Service de Génétique et Embryologie Médicales, Unité Mixte de Recherche_Scientifique 933, Institut National de la Santé et de la Recherche Médicale, Université Pierre et Marie Curie – Paris 6, and Assistance Publique – Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - André Coste
- Unité Mixte de Recherche_Scientifique 855, Institut National de la Santé et de la Recherche Médicale, Université Paris 12, Faculté de Médecine, Créteil, France
- Service d’Otorhinolaryngologie et de chirurgie cervico-faciale, Assistance Publique – Hôpitaux de Paris, Hôpital inter-communal et Groupe Hospitalier Henri Mondor-Albert Chenevier, Créteil, France
| | - Aleksander Edelman
- Unité_1151, Institut National de la Santé et de la Recherche Médicale, Université Paris Descartes, Paris, France
- Plateau Proteome Necker, Structure Fédérative de Recherche de Necker, Université Paris Descartes, Paris, France
- * E-mail:
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14
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Abstract
Proteomics was initially viewed as a promising new scientific discipline to study complex disorders such as polygenic, infectious and environment-related diseases. However, the first attempts to understand a monogenic disease such as cystic fibrosis (CF) by proteomics-based approaches have proved quite rewarding. In CF, the impairment of a unique protein, the CF transmembrane conductance regulator, does not completely explain the complex and variable CF clinical phenotype. The great advances in our knowledge about the molecular and cellular consequences of such impairment have not been sufficient to be translated into effective treatments, and CF patients are still dying due to chronic progressive lung dysfunction. The progression of proteomics application in CF will certainly unravel new proteins that could be useful as biomarkers either to elucidate CF basic mechanisms and to better monitor the disease progression, or to promote the development of novel therapeutic strategies against CF. This review will summarize the recent technological advances in proteomics and the first results of its application to address the most important issues in the CF field.
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Affiliation(s)
- Deborah Penque
- Instituto Nacional de Saúde Dr Ricardo Jorge, Laboratório de Proteómica, Centro de Genética Humana, Lisboa, Portugal.
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15
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Martins LMS, de Andrade HM, Vainstein MH, Wanke B, Schrank A, Balaguez CB, dos Santos PR, Santi L, Pires SDF, da Silva AS, de Castro JAF, Brandão RMSDS, do Monte SJH. Immunoproteomics and immunoinformatics analysis of Cryptococcus gattii: novel candidate antigens for diagnosis. Future Microbiol 2013; 8:549-63. [PMID: 23534365 DOI: 10.2217/fmb.13.22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
AIM To identify immunoreactive proteins of Cryptococcus gattii genotype VGII and their B-cell epitopes. MATERIALS & METHODS We combined 2D gel electrophoresis, immunoblotting and mass spectrometry to identify immunoreactive proteins from four strains of C. gattii genotype VGII (CG01, CG02, CG03 and R265). Next, we screened the identified proteins to map B-cell epitopes. RESULTS Sixty-eight immunoreactive proteins were identified. The strains and the number of proteins we found were: CG01 (12), CG02 (12), CG03 (18) and R265 (26). In addition, we mapped 374 peptides potentially targeted by B cells. CONCLUSION Both immunoreactive proteins and B-cell epitopes of C. gattii genotype VGII that were potentially targeted by a host humoral response were identified. Considering the evolutionary relevance of the identified proteins, we may speculate that they could be used as the initial targets for recombinant protein and peptide synthesis aimed at the development of immunodiagnostic tools for cryptococcosis.
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Affiliation(s)
- Liline Maria Soares Martins
- Laboratório de Imunogenética e Biologia Molecular, Universidade Federal do Piauí, Campus Ministro Petrônio Portella Bloco SG-16, 64049-550, Teresina, Piauí, Brazil.
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16
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Zhang L, Wang Q, Wang W, Liu Y, Wang J, Yue J, Xu Y, Xu W, Cui Z, Zhang X, Wang H. Identification of putative biomarkers for the serodiagnosis of drug-resistant Mycobacterium tuberculosis. Proteome Sci 2012; 10:12. [PMID: 22364187 PMCID: PMC3305424 DOI: 10.1186/1477-5956-10-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2011] [Accepted: 02/25/2012] [Indexed: 02/02/2023] Open
Abstract
Background Early diagnosis and treatment of Mycobacterium tuberculosis infection can prevent most deaths resulting from this pathogen; however, multidrug-resistant strains present serious threats to global tuberculosis control and prevention efforts. In this study, we identified antigens that could be used for the serodiagnosis of drug-resistant M. tuberculosis strains, using a proteomics-based analysis. Results Serum from patients infected with drug-resistant or drug-susceptible M. tuberculosis strains and healthy controls was subjected to two-dimensional gel electrophoresis using a western blot approach. This procedure identified nine immunoreactive proteins, which were subjected to MALDI-TOF-MS analysis. Six recombinant proteins, namely rRv2031c, rRv0444c, rRv2145c, rRv3692, rRv0859c, and rRv3040, were expressed and used to determine the immuno-reactivity of 100 serum samples. Antibody reactivity against rRv2031c, rRv3692, and rRv0444c was consistently observed. Among them, the best sensitivity and specificity of rRv3692 were 37% and 95% respectively. Furthermore, when rRv2031c and rRv3692 or rRv2031c, rRv3692, and rRv0444c were combined in 2:1 or equal amounts, the assay sensitivity and specificity were improved to 56.7% and 100% respectively. Conclusions These results suggest that Rv2031c, Rv3692, and Rv0444c are possible candidate biomarkers for effective use in the serodiagnosis of drug-resistant tuberculosis infections, and a combined formula of these antigens should be considered when designing a subunit assay kit.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, 220 Handan Road, 200433 Shanghai, Peoples Republic of China.
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17
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Role of thioredoxin in lung disease. Pulm Pharmacol Ther 2012; 25:154-62. [PMID: 22293327 DOI: 10.1016/j.pupt.2012.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 01/04/2012] [Accepted: 01/05/2012] [Indexed: 12/25/2022]
Abstract
Thioredoxin system is a ubiquitous thiol oxidoreductase system that regulates cellular reduction/oxidation (redox) status. It includes thioredoxin (Trx), thioredoxin reductase (TrxR), and NADPH. Trx plays an essential role in cell function by limiting oxidative stress directly via antioxidant effects and indirectly by proteins interaction with key signal transduction molecules. A variety of signaling molecules have been implicated in the cytoprotection conferred by Trx, such as autophagic proteins, p38 mitogen-activated protein kinase, nuclear factor-κB, phosphatidylinositol 3-kinase. Recent studies indicated that Trx may contribute to the pathogenesis of COPD, asthma and lung injury. Enhanced Trx expression or application of recombinant Trx afforded protection in preclinical models of pulmonary tissue injury, which suggested Trx may be used in future therapeutic applications. The focus of this review is on the significance of Trx in various pulmonary diseases, which as a potential therapeutic strategy to protect against oxidative stress and inflammation.
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18
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Carter CJ. Pathogen and autoantigen homologous regions within the cystic fibrosis transmembrane conductance regulator (CFTR) protein suggest an autoimmune treatable component of cystic fibrosis. ACTA ACUST UNITED AC 2011; 62:197-214. [DOI: 10.1111/j.1574-695x.2011.00803.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Bargagli E, Olivieri C, Cintorino M, Refini RM, Bianchi N, Prasse A, Rottoli P. Calgranulin B (S100A9/MRP14): a key molecule in idiopathic pulmonary fibrosis? Inflammation 2011; 34:85-91. [PMID: 20422274 DOI: 10.1007/s10753-010-9210-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Calgranulin B is a small calcium-binding protein with several immunological functions mainly involved in chronic inflammation and cancer. It can participate in recruitment of neutrophils and leukocytes in inflamed tissue, oxidant/antioxidant balance, adhesion of neutrophils to fibronectin, and regulation of apoptosis. In a previous proteomic study, we found that calgranulin B was up-regulated in the bronchoalveolar lavage (BAL) of patients with idiopathic pulmonary fibrosis (IPF) with respect to controls and patients with other interstitial lung diseases. The aims of this study are to compare calgranulin B concentrations in BAL of patients with IPF and sarcoidosis and controls by a quantitative method, to look for correlations with clinical data, and to evaluate calgranulin B expression in lung tissue of IPF patients by immunohistochemistry. A modification of a commercial ELISA was used to determine calgranulin B concentrations in BAL of 16 patients with IPF (a group of patients in which we previously performed proteomic analysis), 17 patients with sarcoidosis, and 7 controls. The immunohistochemistry was done in a subgroup of patients with IPF and a control group of lung transplant donors. Calgranulin B concentrations were significantly higher in patients with IPF than controls (p < 0.01); they were inversely correlated with FVC and DLCO values and directly correlated with neutrophil and eosinophil percentages in BAL. Immunohistochemistry revealed a patchy distribution of calgranulin B, predominantly around areas of fibrotic remodeling. Calgranulin B may be a trigger molecule involved in the evolution and progression of IPF, being overexpressed in BAL of patients with IPF with severe functional deterioration and in the peribronchiolar area bordering zones of honeycombing.
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Affiliation(s)
- Elena Bargagli
- Respiratory Diseases Section, Dept. of Clinical Medicine and Immunological Sciences, Siena University, Siena, Italy.
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20
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Abstract
Cystic fibrosis is one of the most common life-limiting inherited disorders. Its clinical impact manifests chiefly in the lung, pancreas, gastrointestinal tract and sweat glands, with lung disease typically being most detrimental to health. The median age for survival has increased dramatically over the past decades, largely thanks to advances in understanding of the mechanisms and consequences of disease, leading to the development of better therapies and treatment regimes. The discovery of dysregulated protein biomarkers linked to cystic fibrosis has contributed considerably to this end. This article outlines clinical trials targeting known protein biomarkers, and the current and future contributions of proteomic techniques to cystic fibrosis research. The treatments described range from those designed to provide functional copies of the mutant protein responsible for cystic fibrosis, to others addressing the associated symptoms of chronic inflammation. Preclinical research has employed proteomics to help elucidate pathways and processes implicated in disease that might present opportunities for therapy or prognosis. Global analyses of cystic fibrosis have detected the differential expression of proteins involved in inflammation, proteolytic activity and oxidative stress, which are recognized symptoms of the cystic fibrosis phenotype. The dysregulation of other processes, such as the complement and mitochondrial systems, has also been implicated. A number of studies have focused specifically on proteins that interact with the cystic fibrosis protein, with the goal of restoring its normal proteostasis. Consequently, proteins involved in synthesis, folding, degradation, translocation and localization of the protein have been identified as potential therapeutic targets. Cystic fibrosis patients are prone to lung infections that are thought to contribute to chronic inflammation, and thus proteomic studies have also searched for microbiological biomarkers to use in early infection diagnosis or as indicators of virulence. The review concludes by proposing a future role for proteomics in the high-throughput validation of protein biomarkers under consideration as outcome measures for use in clinical trials and routine disease monitoring.
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21
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Charro N, Hood BL, Faria D, Pacheco P, Azevedo P, Lopes C, de Almeida AB, Couto FM, Conrads TP, Penque D. Serum proteomics signature of cystic fibrosis patients: a complementary 2-DE and LC-MS/MS approach. J Proteomics 2010; 74:110-26. [PMID: 20950718 DOI: 10.1016/j.jprot.2010.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Revised: 09/17/2010] [Accepted: 10/05/2010] [Indexed: 01/01/2023]
Abstract
Complementary 2D-PAGE and 'shotgun' LC-MS/MS approaches were combined to identify medium and low-abundant proteins in sera of Cystic Fibrosis (CF) patients (mild or severe pulmonary disease) in comparison with healthy CF-carrier and non-CF carrier individuals aiming to gain deeper insights into the pathogenesis of this multifactorial genetic disease. 78 differentially expressed spots were identified from 2D-PAGE proteome profiling yielding 28 identifications and postulating the existence of post-translation modifications (PTM). The 'shotgun' approach highlighted altered levels of proteins actively involved in CF: abnormal tissue/airway remodeling, protease/antiprotease imbalance, innate immune dysfunction, chronic inflammation, nutritional imbalance and Pseudomonas aeruginosa colonization. Members of the apolipoproteins family (VDBP, ApoA-I, and ApoB) presented gradually lower expression from non-CF to CF-carrier individuals and from those to CF patients, results validated by an independent assay. The multifunctional enzyme NDKB was identified only in the CF group and independently validated by WB. Its functions account for ion sensor in epithelial cells, pancreatic secretion, neutrophil-mediated inflammation and energy production, highlighting its physiological significance in the context of CF. Complementary proteomics-based approaches are reliable tools to reveal pathways and circulating proteins actively involved in a heterogeneous disease such as CF.
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Affiliation(s)
- Nuno Charro
- Laboratório de Proteómica, Departamento de Genética, INSA, I.P., Lisboa, Portugal
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22
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Abstract
Proteomics has the goal of defining the complete protein complement of biological systems, which can then be analyzed in a comparative fashion to generate informative data regarding protein expression and function. Proteomic analyses can also facilitate the discovery of biomarkers that can be used to diagnose and monitor disease severity, activity and therapeutic response, as well as to identify new targets for drug development. A major challenge for proteomics, however, has been detecting low-abundance proteins in complex biological fluids. This review summarizes how proteomic analyses have advanced lung cell biology and facilitated the identification of new mechanisms of disease pathogenesis in respiratory disorders, such as asthma, cystic fibrosis, lung cancer, acute lung injury and sarcoidosis. The impact of nanotechnology and microfluidics, as well as studies of post-translational modifications and protein-protein interactions (the interactome), are considered. Furthermore, the application of systems-biology approaches to organize and analyze data regarding the lung proteome, interactome, genome, transcriptome, metabolome, glycome and small RNAome (regulatory RNAs), should facilitate future conceptual advances regarding lung cell biology, disease pathogenesis, biomarker discovery and drug development.
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Affiliation(s)
- Stewart J Levine
- National Institutes of Health, Pulmonary-Critical Care Medicine Branch, NHLBI, Building 10, Room 6D03, MSC 1590, Bethesda, MD 0892-1590, USA.
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23
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Santi L, Silva WO, Pinto AF, Schrank A, Vainstein MH. Metarhizium anisopliae host–pathogen interaction: differential immunoproteomics reveals proteins involved in the infection process of arthropods. Fungal Biol 2010; 114:312-9. [DOI: 10.1016/j.funbio.2010.01.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 01/05/2010] [Accepted: 01/22/2010] [Indexed: 11/26/2022]
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24
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Hare NJ, Cordwell SJ. Proteomics of bacterial pathogens: Pseudomonas aeruginosa infections in cystic fibrosis - a case study. Proteomics Clin Appl 2010; 4:228-48. [PMID: 21137046 DOI: 10.1002/prca.200900144] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2009] [Revised: 09/09/2009] [Accepted: 09/30/2009] [Indexed: 12/20/2022]
Abstract
Technology development in the high throughput sciences of genomics, transcriptomics and proteomics, has been driven by bacteriological research. These organisms are excellent models for testing new methodology due to their comparatively small genome size, the relative ease of culturing large amounts of material, and the inherent biomedical, environmental and biotechnological interest in their underlying biology. Techniques developed in prokaryotes have since become applicable to higher organisms and human disease, opening vast research opportunities for understanding complex molecular processes. Pseudomonas aeruginosa is an excellent example of a microbe with fascinating properties suitable for stretching the boundaries of technology, and with underlying biology that remains poorly understood. P. aeruginosa is an opportunistic pathogen in humans and contains one of the largest genetic capabilities for a single-celled organism (approximately 5500 genes), which allows it to encode a wide variety of surface-associated and secreted virulence factors, as well as adapt to harsh environments, forming resistance to an array of antibacterial agents. While it is a major threat as a nosocomial pathogen, and particularly in the immunocompromised, it is also the most significant cause of mortality in patients suffering from the genetic disorder, cystic fibrosis. This review examines the role of proteomics in gaining a better understanding of the molecular basis of P. aeruginosa infection and persistence in the lungs of cystic fibrosis patients.
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Affiliation(s)
- Nathan J Hare
- School of Molecular and Microbial Biosciences, The University of Sydney, Sydney, Australia
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25
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Lau ATY, Chiu JF. Biomarkers of lung-related diseases: current knowledge by proteomic approaches. J Cell Physiol 2009; 221:535-43. [PMID: 19681054 PMCID: PMC7166618 DOI: 10.1002/jcp.21893] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The lung epithelial surface is one of the vital barriers or sensors in the body responding to the external atmosphere and thereby always subjecting to direct toxicological exposure, stress, stimulus, or infection. Due to its relatively higher sensitivity in response to toxicants, the use of lung epithelial cell culture and lung tissue from animal models or patients has facilitated our learning to lung physiopathology and toxicopharmacology. The recent advancement of proteomics has made it possible to investigate the cellular response at a global level. In this review, the potential applications of proteomic approach in studying lung-related diseases and biomarker discovery will be discussed.
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Affiliation(s)
- Andy T Y Lau
- Department of Anatomy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, People's Republic of China
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26
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Immunoproteomics to identify tumor-associated antigens eliciting humoral response. Cancer Lett 2009; 278:123-129. [DOI: 10.1016/j.canlet.2008.09.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 07/15/2008] [Accepted: 09/09/2008] [Indexed: 01/13/2023]
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27
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Stempfer R, Kubicek M, Lang IM, Christa N, Gerner C. Quantitative assessment of human serum high-abundance protein depletion. Electrophoresis 2009; 29:4316-23. [PMID: 18956433 DOI: 10.1002/elps.200800211] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The aim of this study is to quantify the effectivity of the depletion of human high-abundance serum and plasma proteins for improved protein identification and disease marker candidate discovery and to assess the risk of concomitant removal of relevant marker proteins. 2-DE and bottom-up shotgun MS combining 2-D capillary chromatography with MS/MS were applied in parallel for the analysis of fractions resulting from the depletion procedure. For many proteins the factors of enrichment by the depletion were obvious allowing their enhanced detection and identification upon high-abundance protein depletion. Nano-liquid chromatography linked MS allowed the efficient identification of several low-abundant proteins that were not identified on the 2-DE gels. Resolving the fractions that were eluted from the matrix upon depletion indicated unspecific binding of disease relevant proteins in plasma samples from acute myocardial infarction patients. The unspecific binding to the depletion matrix of inflammatory markers spiked into the serum was found to depend on the type of capturing agent used. Polyclonal avian antibodies (IgY) displayed the least unspecific binding due to the high immunogenicity of mammalian proteins in avian hosts.
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Affiliation(s)
- Rene Stempfer
- Molecular Diagnostics, Life Sciences, Austrian Research Centers GmbH - ARC, Seibersdorf, Austria
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28
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Penque D. Two-dimensional gel electrophoresis and mass spectrometry for biomarker discovery. Proteomics Clin Appl 2008; 3:155-72. [DOI: 10.1002/prca.200800025] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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29
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Trzcinska-Daneluti AM, Ly D, Huynh L, Jiang C, Fladd C, Rotin D. High-content functional screen to identify proteins that correct F508del-CFTR function. Mol Cell Proteomics 2008; 8:780-90. [PMID: 19088066 DOI: 10.1074/mcp.m800268-mcp200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cystic Fibrosis is caused by mutations in CFTR, with a deletion of a phenylalanine at position 508 (F508del-CFTR) representing the most common mutation. The F508del-CFTR protein exhibits a trafficking defect and is retained in the endoplasmic reticulum. Here we describe the development of a high-content screen based on a functional assay to identify proteins that correct the F508del-CFTR defect. Using a HEK293 MSR GripTite cell line that stably expresses F508del-CFTR, we individually co-expressed approximately 450 unique proteins fused to the Cl(-)-sensitive YFP(H148Q/I152L) mutant. We then tested correction of F508del-CFTR function by the CI(-)/l(-) exchange method following stimulation with forskolin/IBMX/genistein, using quantitative recordings in multiple individual cells with a high-content (high-throughput) Cellomics KSR imaging system. Using this approach, we identified several known and novel proteins that corrected F508del-CFTR function, including STAT1, Endothelin 1, HspA4, SAPK substrate protein 1, AP2M1, LGALS3/galectin-3, Trk-fused gene, Caveolin 2, PAP/REG3alpha, and others. The ability of these correctors to rescue F508del-CFTR trafficking was then validated by demonstrating their enhancement of maturation (appearance of band C) and by cell surface expression of F508del-CFTR bearing HA tag at the ectodomain using confocal microscopy and flow cytometry. These data demonstrate the utility of high-content analyses for identifying proteins that correct mutant CFTR and discover new proteins that stimulate this correction. This assay can also be utilized for RNAi screens to identify inhibitory proteins that block correction of F508del-CFTR, small molecule, and peptide screens.
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Affiliation(s)
- Agata M Trzcinska-Daneluti
- Program in Cell Biology, The Hospital for Sick Children, and Biochemistry Department, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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31
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Bargagli E, Olivieri C, Prasse A, Bianchi N, Magi B, Cianti R, Bini L, Rottoli P. Calgranulin B (S100A9) Levels in Bronchoalveolar Lavage Fluid of Patients with Interstitial Lung Diseases. Inflammation 2008; 31:351-4. [DOI: 10.1007/s10753-008-9085-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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32
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Ramachandran N, Srivastava S, Labaer J. Applications of protein microarrays for biomarker discovery. Proteomics Clin Appl 2008; 2:1444-59. [PMID: 21136793 DOI: 10.1002/prca.200800032] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2008] [Indexed: 01/18/2023]
Abstract
The search for new biomarkers for diagnosis, prognosis, and therapeutic monitoring of diseases continues in earnest despite dwindling success at finding novel reliable markers. Some of the current markers in clinical use do not provide optimal sensitivity and specificity, with the prostate cancer antigen (PSA) being one of many such examples. The emergence of proteomic techniques and systems approaches to study disease pathophysiology has rekindled the quest for new biomarkers. In particular the use of protein microarrays has surged as a powerful tool for large-scale testing of biological samples. Approximately half the reports on protein microarrays have been published in the last two years especially in the area of biomarker discovery. In this review, we will discuss the application of protein microarray technologies that offer unique opportunities to find novel biomarkers.
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Affiliation(s)
- Niroshan Ramachandran
- Harvard Institute of Proteomics, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Cambridge, MA, USA
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Martínez-López R, Nombela C, Diez-Orejas R, Monteoliva L, Gil C. Immunoproteomic analysis of the protective response obtained from vaccination with Candida albicans ecm33 cell wall mutant in mice. Proteomics 2008; 8:2651-64. [PMID: 18546157 DOI: 10.1002/pmic.200701056] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Systemic candidiasis remains a major cause of disease and death, particularly among immunocompromised patients. The cell wall of Candida albicans defines the interface between host and pathogen and surface proteins are major elicitors of host immune responses during candidiasis. The C. albicans ecm33 mutant (RML2U) presents an altered cell wall, which entails an increase in the outermost protein layer. Vaccination of BALB/c mice with RML2U mutant protected them from a subsequent lethal infection with virulent strain SC5314 in a systemic candidiasis model. Using immunoproteomics (2-DE followed by Immunoblotting) we detected 29 immunoreactive proteins specifically recognized by antibodies from vaccinated mice sera, six of which are described as immunogenic for the first time (Gnd1p, Cit1p, Rpl10Ep, Yst1p, Cys4p, Efb1p). Furthermore, identification of wild type and mutant cell surface proteome (surfome), confirmed us that the mutant surfome presented a larger number of proteins than the wild type. Interestingly, proteins exclusively identified in the mutant surfome (Met6p, Eft2p, Tkl1p, Rpl10Ep, Atp1p, Atp2p) were also detected as immunogenic, supporting the idea that their surface location enhances their immunoprotective capacity.
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Affiliation(s)
- Raquel Martínez-López
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
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Gray RD, MacGregor G, Noble D, Imrie M, Dewar M, Boyd AC, Innes JA, Porteous DJ, Greening AP. Sputum proteomics in inflammatory and suppurative respiratory diseases. Am J Respir Crit Care Med 2008; 178:444-52. [PMID: 18565957 DOI: 10.1164/rccm.200703-409oc] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Markers of inflammatory activity are important for assessment and management of many respiratory diseases. Markers that are currently unrecognized may be more valuable than those presently believed to be useful. OBJECTIVES To identify potential biomarkers of suppurative and inflammatory lung disease in induced sputum samples. METHODS Induced sputum was collected from 20 healthy control subjects, 24 patients with asthma, 24 with chronic obstructive pulmonary disease, 28 with cystic fibrosis (CF), and 19 with bronchiectasis. Twelve patients with CF had sputum sampled before and after antibiotic therapy for an infective exacerbation. The fluid phase of induced sputum was analyzed by surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectroscopy on three protein array surfaces. Some protein markers were selected for identification, and relevant ELISA assays sought. For 12 patients with CF, both SELDI-TOF and ELISA monitored changes in inflammatory responses during infective exacerbations. MEASUREMENTS AND MAIN RESULTS SELDI-TOF identified potential biomarkers that differentiated each of the disease groups from healthy control subjects: at a significance of P < 0.01, there were 105 for asthma, 113 for chronic obstructive pulmonary disease, 381 for CF, and 377 for bronchiectasis. Peaks selected for protein identification yielded calgranulin A, calgranulin B, calgranulin C, Clara cell secretory protein, lysosyme c, proline rich salivary peptide, cystatin s, and hemoglobin alpha. On treatment of an infective CF exacerbation, SELDI-TOF determined falls in levels of calgranulin A and calgranulin B that were mirrored by ELISA-measured falls in calprotectin (heterodimer of calgranulins A and B). CONCLUSIONS Proteomic screening of sputum yields potential biomarkers of inflammation. The early development of a clinically relevant assay from such data is demonstrated.
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Affiliation(s)
- Robert D Gray
- School of Molecular and Clinical Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
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Hirsch J, Ware LB, Matthay MA. Pulmonary Proteomics. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Friedlander AL, Lynch D, Dyar LA, Bowler RP. Phenotypes of chronic obstructive pulmonary disease. COPD 2007; 4:355-84. [PMID: 18027163 DOI: 10.1080/15412550701629663] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The current clinical classification of smoking-related lung disease fails to take into account the heterogeneity of chronic obstructive pulmonary disease (COPD). With an increased understanding of pathophysiologic variation, COPD now clearly represents a spectrum of overlapping diseases with important extrapulmonary consequences. A "phenotype" describes the outward physical manifestations of a particular disease, and compromises anything that is part of the observable structure, function or behavior of an individual. Such phenotypic distinctions in COPD include: frequent exacerbator, pulmonary cachectic, rapid decliner, airways hyperresponsiveness, impaired exercise tolerance, and emphysema versus airways disease. These variable manifestations, each with unique prognostic, clinical and physiologic ramifications, represent distinct phenotypes within COPD. While all of these phenotypes have smoking as a common risk factor, the other risk factors that determine these phenotypes remain poorly understood. An individual smoker has variable expression of each phenotype and there is mounting evidence that COPD phenotypes have different clinical outcomes. These phenotypes can be broadly classified into one of three groups: clinical, physiologic and radiographic. This review presents the evidence for the spectrum of COPD phenotypes with a focused discussion on the pathophysiologic, epidemiologic and clinical significance of each subtype.
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Affiliation(s)
- Adam L Friedlander
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado at Denver and Health Sciences Center, Denver, CO 80206, USA.
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Sagel SD, Chmiel JF, Konstan MW. Sputum biomarkers of inflammation in cystic fibrosis lung disease. PROCEEDINGS OF THE AMERICAN THORACIC SOCIETY 2007; 4:406-17. [PMID: 17652508 PMCID: PMC2647605 DOI: 10.1513/pats.200703-044br] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Accepted: 05/11/2007] [Indexed: 11/20/2022]
Abstract
Pulmonary biomarkers are being used more frequently to monitor disease activity and evaluate response to treatment in individuals with cystic fibrosis (CF). This article summarizes the current state of knowledge of biomarkers of inflammation relevant to CF lung disease, and the tools to measure inflammation, with specific emphasis on sputum. Sputum is a rich, noninvasive source of biomarkers of inflammation and infection. Sputum induction, through the inhalation of hypertonic saline, has expanded the possibilities for monitoring airway inflammation and infection, especially in individuals who do not routinely expectorate sputum. We critically examine the existing data supporting the validity of sputum biomarkers in CF, with an eye toward their application as surrogate endpoints or outcome measures in CF clinical trials. Further validation studies are needed regarding the variability of inflammatory biomarker measurements, and to evaluate how these biomarkers relate to disease severity, and to longitudinal changes in lung function and other clinical endpoints. We highlight the need to incorporate sputum collection, by induction if necessary, and measurement of sputum biomarkers into routine CF clinical care. In the future, pulmonary biomarkers will likely be useful in predicting disease progression, indicating the onset and resolution of a pulmonary exacerbation, and assessing response to current therapies or candidate therapeutics.
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Affiliation(s)
- Scott D Sagel
- Department of Pediatrics, The Children's Hospital and University of Colorado at Denver and Health Sciences Center, Denver, Colorado 80218, USA.
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Tjalsma H, Lasonder E, Schöller-Guinard M, Swinkels DW. Shotgun immunoproteomics to identify disease-associated bacterial antigens: Application to human colon cancer. Proteomics Clin Appl 2007. [DOI: 10.1002/prca.200601018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Leroy B, Roupie V, Noël-Georis I, Rosseels V, Walravens K, Govaerts M, Huygen K, Wattiez R. Antigen discovery: A postgenomic approach to paratuberculosis diagnosis. Proteomics 2007; 7:1164-76. [PMID: 17366477 DOI: 10.1002/pmic.200600988] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Paratuberculosis is a chronic enteritis caused in domestic and wild ruminant species by Mycobacterium avium subsp. paratuberculosis (MAP) that is responsible for major economic losses to the agricultural industry. To date, no satisfactory therapeutic, vaccine, or diagnostic tools are available, globally impairing all control programs. In this study, we have undertaken a large-scale postgenomic analysis of MAP proteins, to identify specific antigens that could potentially improve the diagnosis of paratuberculosis. Two complementary approaches were implemented, the first one consisting in the systematic proteomic identification of proteins present in MAP culture filtrates (CFs), followed by the selection of MAP-specific proteins by BLAST query on available mycobacterial genomes. The resulting database represents the first established secretome of MAP and a useful source of potentially specific antigens. The second approach consisted in the immunoproteomic analysis of both MAP extracts and CFs, using sera from MAP-infected and uninfected cattle. Combining results obtained with both approaches resulted in the identification of 25 candidate diagnostic antigens. Five of these were tested in an ELISA assay for their diagnostic potential, on a limited panel of field sera, and the combination of three of them competed in performance with available commercial assays, reaching a test sensitivity of 94.74% and specificity of 97.92%.
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Affiliation(s)
- Baptiste Leroy
- Department of Proteomics and Protein Biochemistry, University of Mons-Hainaut, Mons, Belgium
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Ollero M, Brouillard F, Edelman A. Cystic fibrosis enters the proteomics scene: New answers to old questions. Proteomics 2006; 6:4084-99. [PMID: 16791827 DOI: 10.1002/pmic.200600028] [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: 11/09/2022]
Abstract
The discovery in 1989 of the gene encoding for the cystic fibrosis transmembrane conductance regulator (CFTR) and its mutation as the primary cause of cystic fibrosis (CF), generated an optimistic reaction with respect to the development of potential therapies. This extraordinary milestone, however, represented only the initial key step in a long path. Many of the mechanisms that govern the pathogenesis of CF, the most commonly inherited lethal pulmonary disorder in Caucasians, remain even today unknown. As a continuation to genomic research, proteomics now offers the unique advantage to examine global alterations in the protein expression patterns of CF cells and tissues. The systematic use of this approach will probably provide new insights into the cellular mechanisms involved in CF dysfunctions, and should ultimately result in the finding of new prognostic markers, and in the generation of new therapies. In this article we review the current status of proteomic research applied to the study of CF, including CFTR-related interactomics, and evaluate the potential of these technologies for future investigations.
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Perez OD, Nolan GP. Phospho-proteomic immune analysis by flow cytometry: from mechanism to translational medicine at the single-cell level. Immunol Rev 2006; 210:208-28. [PMID: 16623773 DOI: 10.1111/j.0105-2896.2006.00364.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding a molecular basis for cellular function is a common goal of biomedicine. The complex and dynamic cellular processes underlying physiological processes become subtly or grossly perturbed in human disease. A primary objective is to demystify this complexity by creating and establishing relevant model systems to study important aspects of human disease. Although significant technological advancements over the last decade in both genomic and proteomic arenas have enabled progress, accessing the complexity of cellular interactions that occur in vivo has been a difficult arena in which to make progress. Moreover, there are extensive challenges in translating research tools to clinical applications. Flow cytometry, over the course of the last 40 years, has revolutionized the field of immunology, in both the basic science and clinical settings, as well as having been instrumental to new and exciting areas of discovery such as stem cell biology. Multiparameter machinery and systems exist now to access the heterogeneity of cellular subsets and enable phenotypic characterization and functional assays to be performed on material from both animal models and humans. This review focuses primarily on the development and application of using activation-state readouts of intracellular activity for phospho-epitopes. We present recent work on how a flow cytometric platform is used to obtain mechanistic insight into cellular processes as well as highlight the clinical applications that our laboratory has explored. Furthermore, this review discusses the challenges faced with processing high-content multidimensional and multivariate data sets. Flow cytometry, as a platform that is well situated in both the research and clinical settings, can contribute to drug discovery as well as having utility for both biomarker and patient-stratification.
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Affiliation(s)
- Omar D Perez
- The Baxter Laboratory for Genetic Pharmacology, Department of Microbiology and Immunology, Stanford University, School of Medicine, Stanford, CA 94305, USA.
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Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov 2006; 5:310-20. [PMID: 16582876 PMCID: PMC1780251 DOI: 10.1038/nrd2006] [Citation(s) in RCA: 508] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The ability to measure the abundance of many proteins precisely and simultaneously in experimental samples is an important, recent advance for static and dynamic, as well as descriptive and predictive, biological research. The value of multiplexed protein measurement is being established in applications such as comprehensive proteomic surveys, studies of protein networks and pathways, validation of genomic discoveries and clinical biomarker development. As standards do not yet exist that bridge all of these applications, the current recommended best practice for validation of results is to approach study design in an iterative process and to integrate data from several measurement technologies. This review describes current and emerging multiplexed protein measurement technologies and their applications, and discusses the remaining challenges in this field.
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Pitarch A, Jiménez A, Nombela C, Gil C. Decoding Serological Response to Candida Cell Wall Immunome into Novel Diagnostic, Prognostic, and Therapeutic Candidates for Systemic Candidiasis by Proteomic and Bioinformatic Analyses. Mol Cell Proteomics 2006; 5:79-96. [PMID: 16195222 DOI: 10.1074/mcp.m500243-mcp200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In an effort to bring novel diagnostic and prognostic biomarkers or even potential targets for vaccine design for systemic candidiasis (SC) into the open, a systematic proteomic approach coupled with bioinformatic analysis was used to decode the serological response to Candida wall immunome in SC patients. Serum levels of IgG antibodies against Candida wall-associated proteins (proteins secreted from protoplasts in active wall regeneration, separated by two-dimensional gel electrophoresis, and identified by mass spectrometry) were measured in 45 SC patients, 57 non-SC patients, and 61 healthy subjects by Western blotting. Two-way hierarchical clustering and principal component analysis of their serum anti-Candida wall antibody expression patterns discriminated SC patients from controls and highlighted the heterogeneity of their expression profiles. Multivariate logistic regression models demonstrated that high levels of antibodies against glucan 1,3-beta-glucosidase (Bgl2p) and the anti-wall phosphoglycerate kinase antibody seropositivity were the only independent predictors of SC. Receiver operating characteristic curve analysis revealed no difference between their combined evaluation and measurement of anti-Bgl2p antibodies alone. In a logistic regression model adjusted for known prognostic factors for mortality, SC patients with high anti-Bgl2p antibody levels or a positive anti-wall enolase antibody status, which correlated with each other, had a reduced 2-month risk of death. After controlling for each other, only the seropositivity for anti-wall enolase antibodies was an independent predictor of a lower risk of fatality, supporting that these mediated the protective effect. No association between serum anti-cytoplasmic enolase antibody levels and outcomes was established, suggesting a specific mechanism of enolase processing during wall biogenesis. We conclude that serum anti-Bgl2p antibodies are a novel accurate diagnostic biomarker for SC and that, at high levels, they may provide protection by modulating the anti-wall enolase antibody response. Furthermore serum anti-wall enolase antibodies are a new prognostic indicator for SC and confer protection against it. Bgl2p and wall-associated enolase could be valuable candidates for future vaccine development.
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MESH Headings
- Aged
- Antibodies, Fungal/blood
- Antigens, Fungal/immunology
- Candida albicans/immunology
- Candidiasis/immunology
- Candidiasis/therapy
- Case-Control Studies
- Cell Wall/immunology
- Computational Biology
- Databases, Protein
- Electrophoresis, Gel, Two-Dimensional
- Female
- Fungal Proteins/immunology
- Glucan 1,3-beta-Glucosidase/immunology
- Humans
- Immunoglobulin G/blood
- Male
- Phosphopyruvate Hydratase/immunology
- Proteomics
- Sensitivity and Specificity
- Spectrometry, Mass, Electrospray Ionization
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Affiliation(s)
- Aida Pitarch
- Department of Microbiology II, Faculty of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
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