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Ramsey KA, Schultz A, Stick SM. Biomarkers in Paediatric Cystic Fibrosis Lung Disease. Paediatr Respir Rev 2015; 16:213-8. [PMID: 26051089 DOI: 10.1016/j.prrv.2015.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 01/15/2023]
Abstract
Biomarkers in cystic fibrosis are used i. for the measurement of cystic fibrosis transmembrane regulator function in order to diagnose cystic fibrosis, and ii. to assess aspects of lung disease severity (e.g. inflammation, infection). Effective biomarkers can aid disease monitoring and contribute to the development of new therapies. The tests of cystic fibrosis transmembrane regulator function each have unique strengths and weaknesses, and biomarkers of inflammation, infection and tissue destruction have the potential to enhance the management of cystic fibrosis through the early detection of disease processes. The development of biomarkers of cystic fibrosis lung disease, in particular airway inflammation and infection, is influenced by the challenges of obtaining relevant samples from infants and children for whom early detection and treatment of disease might have the greatest long term benefits.
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Affiliation(s)
- Kathryn A Ramsey
- Telethon Kids Institute, University of Western Australia, Australia; Cystic Fibrosis/Pulmonary Research and Treatment Center, University of North Carolina at Chapel Hill, North Carolina, USA
| | - André Schultz
- Telethon Kids Institute, University of Western Australia, Australia; Princess Margaret Hospital for Children, Western Australia, Australia; School of Paediatric and Child Health, University of Western Australia, Australia
| | - Stephen M Stick
- Telethon Kids Institute, University of Western Australia, Australia; Princess Margaret Hospital for Children, Western Australia, Australia; School of Paediatric and Child Health, University of Western Australia, Australia.
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Digestive system dysfunction in cystic fibrosis: challenges for nutrition therapy. Dig Liver Dis 2014; 46:865-74. [PMID: 25053610 DOI: 10.1016/j.dld.2014.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 06/10/2014] [Accepted: 06/28/2014] [Indexed: 02/08/2023]
Abstract
Cystic fibrosis can affect food digestion and nutrient absorption. The underlying mutation of the cystic fibrosis trans-membrane regulator gene depletes functional cystic fibrosis trans-membrane regulator on the surface of epithelial cells lining the digestive tract and associated organs, where Cl(-) secretion and subsequently secretion of water and other ions are impaired. This alters pH and dehydrates secretions that precipitate and obstruct the lumen, causing inflammation and the eventual degradation of the pancreas, liver, gallbladder and intestine. Associated conditions include exocrine pancreatic insufficiency, impaired bicarbonate and bile acid secretion and aberrant mucus formation, commonly leading to maldigestion and malabsorption, particularly of fat and fat-soluble vitamins. Pancreatic enzyme replacement therapy is used to address this insufficiency. The susceptibility of pancreatic lipase to acidic and enzymatic inactivation and decreased bile availability often impedes its efficacy. Brush border digestive enzyme activity and intestinal uptake of certain disaccharides and amino acids await clarification. Other complications that may contribute to maldigestion/malabsorption include small intestine bacterial overgrowth, enteric circular muscle dysfunction, abnormal intestinal mucus, and intestinal inflammation. However, there is some evidence that gastric digestive enzymes, colonic microflora, correction of fatty acid abnormalities using dietary n-3 polyunsaturated fatty acid supplementation and emerging intestinal biomarkers can complement nutrition management in cystic fibrosis.
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Balch WE, Yates JR. Application of mass spectrometry to study proteomics and interactomics in cystic fibrosis. Methods Mol Biol 2011; 742:227-247. [PMID: 21547736 DOI: 10.1007/978-1-61779-120-8_14] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) does not function in isolation, but rather in a complex network of protein-protein interactions that dictate the physiology of a healthy cell and tissue and, when defective, the pathophysiology characteristic of cystic fibrosis (CF) disease. To begin to address the organization and operation of the extensive cystic fibrosis protein network dictated by simultaneous and sequential interactions, it will be necessary to understand the global protein environment (the proteome) in which CFTR functions in the cell and the local network that dictates CFTR folding, trafficking, and function at the cell surface. Emerging mass spectrometry (MS) technologies and methodologies offer an unprecedented opportunity to fully characterize both the proteome and the protein interactions directing normal CFTR function and to define what goes wrong in disease. Below we provide the CF investigator with a general introduction to the capabilities of modern mass spectrometry technologies and methodologies with the goal of inspiring further application of these technologies for development of a basic understanding of the disease and for the identification of novel pathways that may be amenable to therapeutic intervention in the clinic.
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Affiliation(s)
- William E Balch
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Gomes-Alves P, Penque D. Proteomics uncovering possible key players in F508del-CFTR processing and trafficking. Expert Rev Proteomics 2010; 7:487-94. [PMID: 20653505 DOI: 10.1586/epr.10.37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The achievement and maintenance of a protein native conformation is a very complex cellular process involving a multitude of key factors whose contribution to a successful folding remains to be elucidated. On top of this, it is known that correct folding is crucial for proteins to play their normal role and, consequently, for the maintenance of cellular homeostasis or proteostasis. If the folding process is affected, the protein is unable to achieve its native conformation, compromising its life and function, and a pathological condition may arise. Protein-misfolding diseases are characterized by either formation of protein aggregates that are toxic to the cell (gain-of-toxic-function diseases) or by an incorrect processing of proteins, which leads to a deficiency in protein activity (loss-of-function diseases). In this article we have focused on proteomics advances in the molecular knowledge of protein-misfolding diseases with direct impact on possible key players in F508del-CFTR processing and trafficking.
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Affiliation(s)
- Patrícia Gomes-Alves
- Laboratório de Proteómica, Departamento de Genética, Instituto Nacional de Saúde Dr Ricardo Jorge (INSA, I.P.), Av. Padre Cruz, Lisboa, Portugal
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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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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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Gomes-Alves P, Imrie M, Gray RD, Nogueira P, Ciordia S, Pacheco P, Azevedo P, Lopes C, de Almeida AB, Guardiano M, Porteous DJ, Albar JP, Boyd AC, Penque D. SELDI-TOF biomarker signatures for cystic fibrosis, asthma and chronic obstructive pulmonary disease. Clin Biochem 2009; 43:168-77. [PMID: 19850022 DOI: 10.1016/j.clinbiochem.2009.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Revised: 10/09/2009] [Accepted: 10/11/2009] [Indexed: 11/29/2022]
Abstract
OBJECTIVES The aim of this work was to establish protein profiles in serum and nasal epithelial cells of cystic fibrosis individuals in comparison with controls, asthma and chronic obstructive pulmonary disease patients for specific biomarker signatures identification. DESIGN AND METHODS Protein extracts were analyzed by Surface Enhanced Laser Desorption/Ionization Time-Of-Flight Mass-Spectrometry (SELDI-TOF-MS). RESULTS The mass spectra revealed a set of peaks with differential expression in serum and nasal cells among the different groups studied, resulting into peak signatures representative/specific of each pathology. Logistic regressions were applied to those peaks; sensitivity, specificity, Youden's indexes and area under the curve (AUC) of the respective receiver operating characteristic (ROC) curves were compared. DISCUSSION Multivariate analysis demonstrated that combination of peaks has a better predictive value than the individual ones. These protein signatures may serve as diagnostic/prognostic markers for the studied diseases with common clinical features, or as follow-up assessment markers of therapeutic interventions.
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Affiliation(s)
- Patrícia Gomes-Alves
- Laboratório de Proteómica, Departamento de Genética, INSA-IP, Av Padre Cruz, 1649-016 Lisboa, Portugal
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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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Carvalho-Oliveira I, Scholte BJ, Penque D. What have we learned from mouse models for cystic fibrosis? Expert Rev Mol Diagn 2007; 7:407-17. [PMID: 17620048 DOI: 10.1586/14737159.7.4.407] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetically modified mouse strains are important research tools for the study of numerous human diseases. These models provide us with differentiated tissues, which are not often available from human sources. Furthermore, they allow for testing the effects of genetic manipulation and experimental therapeutics on physiology and pathology. Their importance relies on the assumption that biological processes in the mouse very closely resemble those in humans. Cystic fibrosis (CF) is the most common lethal genetic disease in the Caucasian population. CF is a monogenic disease whose phenotype variability is also attributed to genetic variation in other genes, the so-called modifier genes. Modulation of such modifier genes could be a therapeutic strategy to treat CF. CF mice models have been essential not only for understanding the disease better, but also for the discovery of modifier genes and testing of chemical compounds developed to repair the main protein dysfunction in CF, the CF transmembrane conductance regulator. Mice were also indispensable in gene therapy trials and for the study of CF and non-CF lung response to bacterial infections and inflammation challenges, although no spontaneous lung disease is developed in these mice. In this review, mouse models and their most important contribution to the understanding and management of CF will be presented and discussed.
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Affiliation(s)
- Isabel Carvalho-Oliveira
- Instituto Nacional de Saúde Dr Ricardo Jorge, Laboratório de Proteómica, Centro de Genética Humana, Lisboa, Portugal.
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Rottoli P. Proteomics in BAL: improved technique may yield more fish. REVISTA PORTUGUESA DE PNEUMOLOGIA 2007. [DOI: 10.1016/s0873-2159(15)30402-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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