51
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Mourad FH, Yau Y, Wasinger VC, Leong RW. Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models. Dig Dis Sci 2017; 62:2266-2276. [PMID: 28717845 DOI: 10.1007/s10620-017-4673-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 07/04/2017] [Indexed: 12/14/2022]
Abstract
Recently, proteomics studies have provided important information on the role of proteins in health and disease. In the domain of inflammatory bowel disease, proteomics has shed important light on the pathogenesis and pathophysiology of inflammation and has contributed to the discovery of some putative clinical biomarkers of disease activity. By being able to obtain a large number of specimens from multiple sites and control for confounding environmental, genetic, and metabolic factors, proteomics studies using animal models of colitis offered an alternative approach to human studies. Our aim is to review the information and lessons acquired so far from the use of proteomics in animal models of colitis. These studies helped understand the importance of different proteins at different stages of the disease and unraveled the different pathways that are activated or inhibited during the inflammatory process. Expressed proteins related to inflammation, cellular structure, endoplasmic reticulum stress, and energy depletion advanced the knowledge about the reaction of intestinal cells to inflammation and repair. The role of mesenteric lymphocytes, exosomes, and the intestinal mucosal barrier was emphasized in the inflammatory process. In addition, studies in animal models revealed mechanisms of the beneficial effects of some therapeutic interventions and foods or food components on intestinal inflammation by monitoring changes in protein expression and paved the way for some new possible inflammatory pathways to target in the future. Advances in proteomics technology will further clarify the interaction between intestinal microbiota and IBD pathogenesis and investigate the gene-environmental axis of IBD etiology.
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Affiliation(s)
- Fadi H Mourad
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box 113-6044, Hamra, Beirut, 110 32090, Lebanon. .,Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia.
| | - Yunki Yau
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia
| | - Valerie C Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of NSW Australia, Kensington, NSW, 2052, Australia
| | - Rupert W Leong
- Gastroenterology and Liver Services, Concord Repatriation General Hospital, Hospital Road, Concord, NSW, 2137, Australia
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52
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Starr AE, Deeke SA, Ning Z, Chiang CK, Zhang X, Mottawea W, Singleton R, Benchimol EI, Wen M, Mack DR, Stintzi A, Figeys D. Proteomic analysis of ascending colon biopsies from a paediatric inflammatory bowel disease inception cohort identifies protein biomarkers that differentiate Crohn's disease from UC. Gut 2017; 66:1573-1583. [PMID: 27216938 PMCID: PMC5561380 DOI: 10.1136/gutjnl-2015-310705] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/10/2016] [Accepted: 04/25/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Accurate differentiation between Crohn's disease (CD) and UC is important to ensure early and appropriate therapeutic intervention. We sought to identify proteins that enable differentiation between CD and UC in children with new onset IBD. DESIGN Mucosal biopsies were obtained from children undergoing baseline diagnostic endoscopy prior to therapeutic interventions. Using a super-stable isotope labeling with amino acids in cell culture (SILAC)-based approach, the proteomes of 99 paediatric control and biopsies of patients with CD and UC were compared. Multivariate analysis of a subset of these (n=50) was applied to identify novel biomarkers, which were validated in a second subset (n=49). RESULTS In the discovery cohort, a panel of five proteins was sufficient to distinguish control from IBD-affected tissue biopsies with an AUC of 1.0 (95% CI 0.99 to 1.0); a second panel of 12 proteins segregated inflamed CD from UC within an AUC of 0.95 (95% CI 0.86 to 1.0). Application of the two panels to the validation cohort resulted in accurate classification of 95.9% (IBD from control) and 80% (CD from UC) of patients. 116 proteins were identified to have correlation with the severity of disease, four of which were components of the two panels, including visfatin and metallothionein-2. CONCLUSIONS This study has identified two panels of candidate biomarkers for the diagnosis of IBD and the differentiation of IBD subtypes to guide appropriate therapeutic interventions in paediatric patients.
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Affiliation(s)
- Amanda E Starr
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Shelley A Deeke
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cheng-Kang Chiang
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada,Department of Microbiology and Immunology, Mansoura University, Mansoura, Egypt
| | - Ruth Singleton
- Children's Hospital of Eastern Ontario (CHEO) Inflammatory Bowel Disease Centre and CHEO Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Eric I Benchimol
- Children's Hospital of Eastern Ontario (CHEO) Inflammatory Bowel Disease Centre and CHEO Research Institute, University of Ottawa, Ottawa, Ontario, Canada,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada,School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Ming Wen
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - David R Mack
- Children's Hospital of Eastern Ontario (CHEO) Inflammatory Bowel Disease Centre and CHEO Research Institute, University of Ottawa, Ottawa, Ontario, Canada,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
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53
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Bhalla S, Verma R, Kaur H, Kumar R, Usmani SS, Sharma S, Raghava GPS. CancerPDF: A repository of cancer-associated peptidome found in human biofluids. Sci Rep 2017; 7:1511. [PMID: 28473704 PMCID: PMC5431423 DOI: 10.1038/s41598-017-01633-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/03/2017] [Indexed: 01/28/2023] Open
Abstract
CancerPDF (Cancer Peptidome Database of bioFluids) is a comprehensive database of endogenous peptides detected in the human biofluids. The peptidome patterns reflect the synthesis, processing and degradation of proteins in the tissue environment and therefore can act as a gold mine to probe the peptide-based cancer biomarkers. Although an extensive data on cancer peptidome has been generated in the recent years, lack of a comprehensive resource restrains the facility to query the growing community knowledge. We have developed the cancer peptidome resource named CancerPDF, to collect and compile all the endogenous peptides isolated from human biofluids in various cancer profiling studies. CancerPDF has 14,367 entries with 9,692 unique peptide sequences corresponding to 2,230 unique precursor proteins from 56 high-throughput studies for ~27 cancer conditions. We have provided an interactive interface to query the endogenous peptides along with the primary information such as m/z, precursor protein, the type of cancer and its regulation status in cancer. To add-on, many web-based tools have been incorporated, which comprise of search, browse and similarity identification modules. We consider that the CancerPDF will be an invaluable resource to unwind the potential of peptidome-based cancer biomarkers. The CancerPDF is available at the web address http://crdd.osdd.net/raghava/cancerpdf/.
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Affiliation(s)
- Sherry Bhalla
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Ruchi Verma
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Harpreet Kaur
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Rajesh Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Salman Sadullah Usmani
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Suresh Sharma
- Centre for Systems Biology and Bioinformatics, Panjab University, Sector 14, Chandigarh, 160014, India
| | - Gajendra P S Raghava
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.
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Identification of Candidate Genes Related to Inflammatory Bowel Disease Using Minimum Redundancy Maximum Relevance, Incremental Feature Selection, and the Shortest-Path Approach. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5741948. [PMID: 28293637 PMCID: PMC5331171 DOI: 10.1155/2017/5741948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/11/2017] [Indexed: 02/08/2023]
Abstract
Identification of disease genes is a hot topic in biomedicine and genomics. However, it is a challenging problem because of the complexity of diseases. Inflammatory bowel disease (IBD) is an idiopathic disease caused by a dysregulated immune response to host intestinal microflora. It has been proven to be associated with the development of intestinal malignancies. Although the specific pathological characteristics and genetic background of IBD have been partially revealed, it is still an overdetermined disease and the blueprint of all genetic variants still needs to be improved. In this study, a novel computational method was built to identify genes related to IBD. Samples from two subtypes of IBD (ulcerative colitis and Crohn's disease) and normal samples were employed. By analyzing the gene expression profiles of these samples using minimum redundancy maximum relevance and incremental feature selection, 21 genes were obtained that could effectively distinguish samples from the two subtypes of IBD and the normal samples. Then, the shortest-path approach was used to search for an additional 20 genes in a large network constructed using protein-protein interactions based on the above-mentioned 21 genes. Analyses of the 41 genes obtained indicate that they are closely associated with this disease.
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55
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Asadzadeh-Aghdaee H, Shahrokh S, Norouzinia M, Hosseini M, Keramatinia A, Jamalan M, Naghibzadeh B, Sadeghi A, Jahani Sherafat S, Zali MR. Introduction of inflammatory bowel disease biomarkers panel using protein-protein interaction (PPI) network analysis. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2016; 9:S8-S13. [PMID: 28224022 PMCID: PMC5310794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AIM In the present study, a protein-protein interaction network construction is conducted for IBD. BACKGROUND Inflammatory bowel diseases as serious chronic gastrointestinal disorders attracted many molecular investigations. Diverse molecular information is present for IBD. However, these molecular findings are not highlighted based on interactome analysis. On the other hand, PPI network analysis is a powerful method for study of molecular interactions in the protein level that provide useful information for highlighting the desired key proteins. METHODS Cytoscape is the used software with its plug-ins for detailed analysis. Two centrality parameters including degree and betweenness are determined and the crucial proteins based on these parameters are introduced. RESULTS The 75 proteins among 100 initial proteins are included in the network of IBD. Seventy-five nodes and 260 edges constructed the network as a scale free network. The findings indicate that there are seven hub-bottleneck proteins in the IBD network. CONCLUSION More examination revealed the essential roles of these key proteins in the integrity of the network. Finally, the indicator panel including NFKB1, CD40, TNFA, TYK2, NOD2, IL23R, and STAT3 is presented as a possible molecular index for IBD.
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Affiliation(s)
- Hamid Asadzadeh-Aghdaee
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research institute for Gastroenterologyand Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shabnam Shahrokh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research institute for Gastroenterologyand Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Norouzinia
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Hosseini
- Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aliasghar Keramatinia
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bijan Naghibzadeh
- Hearing Disorders Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Sadeghi
- Department of Biomedical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Somayeh Jahani Sherafat
- Behbood Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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56
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Hesselager MO, Codrea MC, Sun Z, Deutsch EW, Bennike TB, Stensballe A, Bundgaard L, Moritz RL, Bendixen E. The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine. Proteomics 2016; 16:634-44. [PMID: 26699206 DOI: 10.1002/pmic.201500195] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 11/02/2015] [Accepted: 12/16/2015] [Indexed: 01/14/2023]
Abstract
Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.
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Affiliation(s)
| | - Marius C Codrea
- Quantitative Biology Center (QBiC), Eberhard Karls Universität, Tübingen, Germany
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Tue B Bennike
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Louise Bundgaard
- Department of Large Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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57
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Witalison EE, Cui X, Causey CP, Thompson PR, Hofseth LJ. Molecular targeting of protein arginine deiminases to suppress colitis and prevent colon cancer. Oncotarget 2016; 6:36053-62. [PMID: 26440311 PMCID: PMC4742161 DOI: 10.18632/oncotarget.5937] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 09/16/2015] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic disease, in which the lining of the colon becomes inflamed and develops ulcers leading to abdominal pain, diarrhea, and rectal bleeding. The extent of these symptoms depends on disease severity. The protein arginine deiminase (PAD) family of enzymes converts peptidyl-Arginine to peptidyl-Citrulline through citrullination. PADs are dysregulated, with abnormal citrullination in many diseases, including UC and colorectal cancer (CRC). We have developed the small molecule, pan-PAD inhibitor, Chlor-amidine (Cl-amidine), with multiple goals, including treating UC and preventing CRC. Building off our recent results showing that: 1) Cl-amidine suppresses colitis in vivo in a dextran sulfate sodium (DSS) mouse model; and 2) Cl-amidine induces microRNA (miR)-16 in vitro causing cell cycle arrest, we tested the hypothesis that Cl-amidine can prevent tumorigenesis and that miR-16 induction, by Cl-amidine, may be involved in vivo. Consistent with our hypothesis, we present evidence that Cl-amidine, delivered in the drinking water, prevents colon tumorigenesis in our mouse model of colitis-associated CRC where mice are given carcinogenic azoxymethane (AOM), followed by multiple cycles of 2% DSS to induce colitis. To begin identifying mechanisms, we examined the effects of Cl-amidine on miR-16. Results show miR-16 suppression during the colitis-to-cancer sequence in colon epithelial cells, which was rescued by drinking Cl-amidine. Likewise, Ki67 and cellular proliferation targets of miR-16 (Cyclins D1 and E1) were suppressed by Cl-amidine. The decrease in cell proliferation markers and increase in tumor suppressor miRNA expression potentially define a mechanism of how Cl-amidine is suppressing tumorigenesis in vivo.
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Affiliation(s)
- Erin E Witalison
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Xiangli Cui
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA.,Shanxi Medical University, Taiyun, China
| | - Corey P Causey
- Department of Chemistry, University of North Florida, Jacksonville, FL, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lorne J Hofseth
- Department of Drug Discovery and Biomedical Sciences, South Carolina College of Pharmacy, University of South Carolina, Columbia, SC, USA
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58
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Licier R, Miranda E, Serrano H. A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples. Proteomes 2016; 4:proteomes4040031. [PMID: 28248241 PMCID: PMC5260964 DOI: 10.3390/proteomes4040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 01/13/2023] Open
Abstract
The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.
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Affiliation(s)
- Rígel Licier
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico.
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
| | - Eric Miranda
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
| | - Horacio Serrano
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
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59
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Iborra M, Beltrán B, Nos P. Noninvasive Testing for Mucosal Inflammation in Inflammatory Bowel Disease. Gastrointest Endosc Clin N Am 2016; 26:641-56. [PMID: 27633593 DOI: 10.1016/j.giec.2016.06.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Biomarkers have gained increasing attention for the diagnosis and follow-up of inflammatory bowel disease (IBD). Endoscopy remains the gold standard for assessing disease activity. Biomarkers are rapid, inexpensive, and noninvasive, and can be used in different stages of the disease with high sensitivity and specificity. Calprotectin and tests for C-reactive protein are used to assess the disease activity, predict relapse, and monitor treatment response. New noninvasive tests are being studied. This review discusses current evidence for these surrogate markers, their potential clinical applications, and limitations in disease management. We highlight recent advances in IBD biomarkers and future uses.
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Affiliation(s)
- Marisa Iborra
- Gastroenterology Department, Department of Digestive Disease, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell, 106, Valencia 46026, Spain
| | - Belén Beltrán
- Gastroenterology Department, Department of Digestive Disease, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell, 106, Valencia 46026, Spain
| | - Pilar Nos
- Gastroenterology Department, Department of Digestive Disease, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), La Fe University and Polytechnic Hospital, Av. Fernando Abril Martorell, 106, Valencia 46026, Spain.
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Bennike TB, Ellingsen T, Glerup H, Bonderup OK, Carlsen TG, Meyer MK, Bøgsted M, Christiansen G, Birkelund S, Andersen V, Stensballe A. Proteome Analysis of Rheumatoid Arthritis Gut Mucosa. J Proteome Res 2016; 16:346-354. [PMID: 27627584 DOI: 10.1021/acs.jproteome.6b00598] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Rheumatoid arthritis (RA) is an inflammatory joint disease leading to cartilage damage and ultimately impaired joint function. To gain new insight into the systemic immune manifestations of RA, we characterized the colon mucosa proteome from 11 RA-patients and 10 healthy controls. The biopsies were extracted by colonoscopy and analyzed by label-free quantitative proteomics, enabling the quantitation of 5366 proteins. The abundance of dihydrofolate reductase (DHFR) was statistically significantly increased in RA-patient biopsies compared with controls and correlated with the administered dosage of methotrexate (MTX), the most frequently prescribed immunosuppressive drug for RA. Additionally, our data suggest that treatment with Leflunomide, a common alternative to MTX, increases DHFR. The findings were supported by immunohistochemistry with confocal microscopy, which furthermore demonstrated that DHFR was located in the cytosol of the intestinal epithelial and interstitial cells. Finally, we identified 223 citrullinated peptides from 121 proteins. Three of the peptides were unique to RA. The list of citrullinated proteins was enriched in extracellular and membrane proteins and included known targets of anticitrullinated protein antibodies (ACPAs). Our findings support that the colon mucosa could trigger the production of ACPAs, which could contribute to the onset of RA. The MS data have been deposited to ProteomeXchange with identifiers PXD001608 and PXD003082.
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Affiliation(s)
- Tue Bjerg Bennike
- Departments of Pathology, Boston Children's Hospital and Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Torkell Ellingsen
- Department of Rheumatology, Odense University Hospital , Odense DK-5000, Denmark.,University Research Clinic for Innovative Patient Pathways, Aarhus University , Aarhus DK- 8000, Denmark
| | - Henning Glerup
- University Research Clinic for Innovative Patient Pathways, Aarhus University , Aarhus DK- 8000, Denmark.,Diagnostic Center, Section of Gastroenterology, Regional Hospital Silkeborg , Silkeborg DK-8600, Denmark
| | - Ole Kristian Bonderup
- University Research Clinic for Innovative Patient Pathways, Aarhus University , Aarhus DK- 8000, Denmark.,Diagnostic Center, Section of Gastroenterology, Regional Hospital Silkeborg , Silkeborg DK-8600, Denmark
| | - Thomas Gelsing Carlsen
- Department of Health Science and Technology, Aalborg University , Aalborg DK-9220, Denmark
| | - Michael Kruse Meyer
- Department of Health Science and Technology, Aalborg University , Aalborg DK-9220, Denmark.,Department of Rheumatology and Center for Clinical Research, North Denmark Regional Hospital , Hjoerring DK-9800, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University , Aalborg DK-9220, Denmark.,Department of Haematology, Aalborg University Hospital , Aalborg DK-9000, Denmark
| | | | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University , Aalborg DK-9220, Denmark
| | - Vibeke Andersen
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark , Odense DK-5230, Denmark.,Molecular Diagnostic and Clinical Research Unit, Hospital of Southern Jutland , Aabenraa DK-6200, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University , Aalborg DK-9220, Denmark
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61
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Coit P, Sawalha AH. The human microbiome in rheumatic autoimmune diseases: A comprehensive review. Clin Immunol 2016; 170:70-9. [DOI: 10.1016/j.clim.2016.07.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 07/30/2016] [Indexed: 12/17/2022]
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62
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Griendling KK, Touyz RM, Zweier JL, Dikalov S, Chilian W, Chen YR, Harrison DG, Bhatnagar A. Measurement of Reactive Oxygen Species, Reactive Nitrogen Species, and Redox-Dependent Signaling in the Cardiovascular System: A Scientific Statement From the American Heart Association. Circ Res 2016; 119:e39-75. [PMID: 27418630 DOI: 10.1161/res.0000000000000110] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reactive oxygen species and reactive nitrogen species are biological molecules that play important roles in cardiovascular physiology and contribute to disease initiation, progression, and severity. Because of their ephemeral nature and rapid reactivity, these species are difficult to measure directly with high accuracy and precision. In this statement, we review current methods for measuring these species and the secondary products they generate and suggest approaches for measuring redox status, oxidative stress, and the production of individual reactive oxygen and nitrogen species. We discuss the strengths and limitations of different methods and the relative specificity and suitability of these methods for measuring the concentrations of reactive oxygen and reactive nitrogen species in cells, tissues, and biological fluids. We provide specific guidelines, through expert opinion, for choosing reliable and reproducible assays for different experimental and clinical situations. These guidelines are intended to help investigators and clinical researchers avoid experimental error and ensure high-quality measurements of these important biological species.
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63
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de Bruyn M, Vandooren J, Ugarte-Berzal E, Arijs I, Vermeire S, Opdenakker G. The molecular biology of matrix metalloproteinases and tissue inhibitors of metalloproteinases in inflammatory bowel diseases. Crit Rev Biochem Mol Biol 2016; 51:295-358. [DOI: 10.1080/10409238.2016.1199535] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. EUPA OPEN PROTEOMICS 2016; 10:9-18. [PMID: 29900094 PMCID: PMC5988570 DOI: 10.1016/j.euprot.2015.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/19/2015] [Accepted: 10/25/2015] [Indexed: 01/14/2023]
Abstract
Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics. We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.
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Key Words
- CAN, acetonitrile
- DF, directly-frozen
- FA, formic acid
- FASP, filter-aided sample preparation
- FDR, false discovery rate
- FFPE, formalin-fixed
- Formalin-fixed
- HLA-A class I, histocompatibility antigen A-23 alpha chain
- HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain
- Human colon mucosa
- LFQ, label-free quantification
- Mass spectrometry
- PCA, principle component analysis
- PSM, peptide spectral match
- PTM, post-translational modification
- Paraffin-embedded
- Preservation
- Proteomics
- RNAlater
- SDC, sodium deoxycholate
- SDS, sodium dodecyl sulfate
- TEAB, triethylammonium bicarbonate
- iFFPE, immediately formalin-fixed
- s, standard deviation
- sFFPE, stored for 30 min prior to formalin-fixed
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Affiliation(s)
- Tue Bjerg Bennike
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Simona Padurariu
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A. Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies. Data Brief 2016; 6:942-7. [PMID: 26937473 PMCID: PMC4753390 DOI: 10.1016/j.dib.2016.01.061] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 01/23/2016] [Accepted: 01/27/2016] [Indexed: 02/07/2023] Open
Abstract
Large repositories of well characterized RNAlater preserved samples and formalin-fixed, paraffin-embedded samples have been generated worldwide. However, the impact on the proteome of the preservation methods remain poorly described. Therefore, we analyzed the impact on the proteome of preserving samples in RNAlater, and by formalin-fixation, paraffin-embedding on human soft tissue, using directly frozen samples as a control (“Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples” [1]). We here report the data from the analysis. The comparative analysis was performed on 24 colon mucosa biopsies, extracted from the sigmoideum of two gastroenterologically healthy participants for the purpose of this study. A set of biopsies were additionally stored for 30 min at room temperature prior to formalin-fixation. The samples were analyzed by high throughput gel free quantitative proteomics. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PRIDE: PXD002029.
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Affiliation(s)
- Tue Bjerg Bennike
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark; Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Simona Padurariu
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark; Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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Ferguson LR. Nutritional Modulation of Gene Expression: Might This be of Benefit to Individuals with Crohn's Disease? Front Immunol 2015; 6:467. [PMID: 26441972 PMCID: PMC4566049 DOI: 10.3389/fimmu.2015.00467] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/27/2015] [Indexed: 12/18/2022] Open
Abstract
The incidence of inflammatory bowel diseases (IBD), including Crohn's disease (CD), is increasing worldwide, especially in young children and adolescents. Although hospitalized patients are usually provided with enteral or parenteral support, continuing care typically requires a trial-and-error approach to suppressing symptoms and maintaining disease remission. Current nutritional advice does not differ from general population guidelines. International collaborative studies have revealed 163 distinct genetic loci affecting susceptibility to IBD, in some of which host-microbe interactions can be seen to play an important role. The nature of these loci enables a rationale for predicting nutritional requirements that may not be evident through standard therapeutic approaches. Certain recognized nutrients, such as vitamin D and long-chain omega-3 polyunsaturated fatty acids, may be required at higher than anticipated levels. Various phytochemicals, not usually considered in the same class as classic nutrients, could play an important role. Prebiotics and probiotics may also be beneficial. Genomic approaches enable proof of principle of nutrient optimization rather than waiting for disease symptoms to appear and/or progress. We suggest a paradigm shift in diagnostic tools and nutritional therapy for CD, involving a systems biology approach for implementation.
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Affiliation(s)
- Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, Faculty of Medical and Health Sciences, The University of Auckland , Auckland , New Zealand ; Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland , Auckland , New Zealand
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Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome. Data Brief 2015; 5:241-7. [PMID: 26543887 PMCID: PMC4589796 DOI: 10.1016/j.dib.2015.08.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 08/23/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022] Open
Abstract
Synovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein concentration, content, and synovial fluid volume change dramatically during active joint diseases and inflammation, and the proteome composition of healthy synovial fluid is incompletely characterized. We performed a normative proteomics analysis of porcine synovial fluid, and report data from optimizing proteomic methods to investigate the proteome of healthy porcine synovial fluid (Bennike et al., 2014 [1]). We included an evaluation of different proteolytic sample preparation techniques, and an analysis of posttranslational modifications with a focus on glycosylation. We used pig (Sus Scrofa) as a model organism, as the porcine immune system is highly similar to human and the pig genome is sequenced. Furthermore, porcine model systems are commonly used large animal models to study several human diseases. In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD000935.
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Bennike TB, Carlsen TG, Ellingsen T, Bonderup OK, Glerup H, Bøgsted M, Christiansen G, Birkelund S, Stensballe A, Andersen V. Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies. Inflamm Bowel Dis 2015; 21:2052-67. [PMID: 25993694 PMCID: PMC4603666 DOI: 10.1097/mib.0000000000000460] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/27/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND The etiology of the inflammatory bowel diseases, including ulcerative colitis (UC), remains incompletely explained. We hypothesized that an analysis of the UC colon proteome could reveal novel insights into the disease etiology. METHODS Mucosal colon biopsies were taken by endoscopy from noninflamed tissue of 10 patients with UC and 10 controls. The biopsies were either snap-frozen for protein analysis or prepared for histology. The protein content of the biopsies was characterized by high-throughput gel-free quantitative proteomics, and biopsy histology was analyzed by light microscopy and confocal microscopy. RESULTS We identified and quantified 5711 different proteins with proteomics. The abundance of the proteins calprotectin and lactotransferrin in the tissue correlated with the degree of tissue inflammation as determined by histology. However, fecal calprotectin did not correlate. Forty-six proteins were measured with a statistically significant differences in abundances between the UC colon tissue and controls. Eleven of the proteins with increased abundances in the UC biopsies were associated with neutrophils and neutrophil extracellular traps. The findings were validated by microscopy, where an increased abundance of neutrophils and the presence of neutrophil extracellular traps by extracellular DNA present in the UC colon tissue were confirmed. CONCLUSIONS Neutrophils, induced neutrophil extracellular traps, and several proteins that play a part in innate immunity are all increased in abundance in the morphologically normal colon mucosa from patients with UC. The increased abundance of these antimicrobial compounds points to the stimulation of the innate immune system in the etiology of UC.
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Affiliation(s)
- Tue Bjerg Bennike
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
- Organ Center, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | | | - Torkell Ellingsen
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Ole Kristian Bonderup
- Diagnostic Center, Section of Gastroenterology, Regional Hospital Silkeborg, Silkeborg, Denmark
- University Research Clinic for Innovative Patient Pathways, Aarhus University, Aarhus, Denmark
| | - Henning Glerup
- Diagnostic Center, Section of Gastroenterology, Regional Hospital Silkeborg, Silkeborg, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Organ Center, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
- Department of Internal Medicine, Regional Hospital Viborg, Viborg, Denmark
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69
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Hicks LC, Huang J, Kumar S, Powles ST, Orchard TR, Hanna GB, Williams HRT. Analysis of Exhaled Breath Volatile Organic Compounds in Inflammatory Bowel Disease: A Pilot Study. J Crohns Colitis 2015; 9:731-7. [PMID: 26071410 DOI: 10.1093/ecco-jcc/jjv102] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/01/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Distinguishing between the inflammatory bowel diseases [IBD], Crohn's disease [CD] and ulcerative colitis [UC], is important for determining management and prognosis. Selected ion flow tube mass spectrometry [SIFT-MS] may be used to analyse volatile organic compounds [VOCs] in exhaled breath: these may be altered in disease states, and distinguishing breath VOC profiles can be identified. The aim of this pilot study was to identify, quantify, and analyse VOCs present in the breath of IBD patients and controls, potentially providing insights into disease pathogenesis and complementing current diagnostic algorithms. METHODS SIFT-MS breath profiling of 56 individuals [20 UC, 18 CD, and 18 healthy controls] was undertaken. Multivariate analysis included principal components analysis and partial least squares discriminant analysis with orthogonal signal correction [OSC-PLS-DA]. Receiver operating characteristic [ROC] analysis was performed for each comparative analysis using statistically significant VOCs. RESULTS OSC-PLS-DA modelling was able to distinguish both CD and UC from healthy controls and from one other with good sensitivity and specificity. ROC analysis using combinations of statistically significant VOCs [dimethyl sulphide, hydrogen sulphide, hydrogen cyanide, ammonia, butanal, and nonanal] gave integrated areas under the curve of 0.86 [CD vs healthy controls], 0.74 [UC vs healthy controls], and 0.83 [CD vs UC]. CONCLUSIONS Exhaled breath VOC profiling was able to distinguish IBD patients from controls, as well as to separate UC from CD, using both multivariate and univariate statistical techniques.
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Affiliation(s)
- Lucy C Hicks
- Gastroenterology & Hepatology Section, Department of Medicine, Imperial College London, London UK
| | - Juzheng Huang
- Department of Surgery and Cancer, Imperial College London, London UK
| | - Sacheen Kumar
- Department of Surgery and Cancer, Imperial College London, London UK
| | - Sam T Powles
- Gastroenterology & Hepatology Section, Department of Medicine, Imperial College London, London UK
| | - Timothy R Orchard
- Gastroenterology & Hepatology Section, Department of Medicine, Imperial College London, London UK
| | - George B Hanna
- Department of Surgery and Cancer, Imperial College London, London UK
| | - Horace R T Williams
- Gastroenterology & Hepatology Section, Department of Medicine, Imperial College London, London UK
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C. JAIMELUBASCHER. ERRORES FRECUENTES EN EL DIAGNÓSTICO Y TRATAMIENTO DE LOS PACIENTES CON ENFERMEDAD INFLAMATORIA INTESTINAL. REVISTA MÉDICA CLÍNICA LAS CONDES 2015. [DOI: 10.1016/j.rmclc.2015.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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71
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Soluble Syndecan-1: Does This Biomarker Address a Seemingly Insoluble Problem in Inflammatory Bowel Disease? Dig Dis Sci 2015; 60:2222-4. [PMID: 25911586 DOI: 10.1007/s10620-015-3669-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 04/10/2015] [Indexed: 01/12/2023]
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Diagnosis of Irritable Bowel Syndrome: Role of Potential Biomarkers. Gastroenterol Res Pract 2015; 2015:490183. [PMID: 26170833 PMCID: PMC4480928 DOI: 10.1155/2015/490183] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/26/2015] [Indexed: 12/15/2022] Open
Abstract
Irritable bowel syndrome is a disorder diagnosed on symptom-based criteria without inclusion of any objective parameter measurable by known diagnostic methods. Heterogeneity of the disorder and overlapping with more serious organic diseases increase uncertainty for the physician's work and increase the cost of confirming the diagnosis. This paper is an attempt to summarize the efforts to find adequate biomarkers for irritable bowel syndrome, which should shorten the time to diagnosis and reduce the cost. Most of the reviewed papers were observational studies from secondary care institutions. Since publication of the Rome III criteria in 2006, most recent studies use these for the recruitment of IBS patients. This is a positive step forward as future studies should use the same criteria, facilitating comparison of their results. Among the studied biomarkers, most evidence is provided for fecal calprotectin. Cutoff values for fecal calprotectin have still to be investigated prior to inclusion in the irritable bowel syndrome diagnostic algorithm.
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Abstract
All of life is regulated by complex and organized chemical reactions that help dictate when to grow, to move, to reproduce, and to die. When these processes go awry, or are interrupted by pathological agents, diseases such as cancer, autoimmunity, or infections can result. Cytokines, chemokines, growth factors, adipokines, and other chemical moieties make up a vast subset of these chemical reactions that are altered in disease states, and monitoring changes in these molecules could provide for the identification of disease biomarkers. From the first identification of carcinoembryonic antigen, to the discovery of prostate-specific antigen, to numerous others described within, biomarkers of disease are detectable in a plethora of sample types. The growing number of biomarkers for infection, autoimmunity, and cancer allow for increasingly early detection, to identification of novel drug targets, to prognostic indicators of disease outcome. However, more and more studies are finding that a single cytokine or growth factor is insufficient as a true disease biomarker and that a more global perspective is needed to understand true disease biology. Such a broad view requires a multiplexed platform for chemical detection, and antibody arrays meet and exceed this need by performing this detection in a high-throughput fashion. Herein, we will discuss how antibody arrays have evolved, and how they have helped direct new drug target design, helped identify therapeutic disease markers, and helped in earlier disease detection. From asthma to renal disease, and neurological dysfunction to immunologic disorders, antibody arrays afford a bright future for new biomarkers discovery.
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74
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Tontini GE, Vecchi M, Pastorelli L, Neurath MF, Neumann H. Differential diagnosis in inflammatory bowel disease colitis: State of the art and future perspectives. World J Gastroenterol 2015; 21:21-46. [PMID: 25574078 PMCID: PMC4284336 DOI: 10.3748/wjg.v21.i1.21] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 07/31/2014] [Accepted: 09/16/2014] [Indexed: 02/06/2023] Open
Abstract
Distinction between Crohn’s disease of the colon-rectum and ulcerative colitis or inflammatory bowel disease (IBD) type unclassified can be of pivotal importance for a tailored clinical management, as each entity often involves specific therapeutic strategies and prognosis. Nonetheless, no gold standard is available and the uncertainty of diagnosis may frequently lead to misclassification or repeated examinations. Hence, we have performed a literature search to address the problem of differential diagnosis in IBD colitis, revised current and emerging diagnostic tools and refined disease classification strategies. Nowadays, the differential diagnosis is an untangled issue, and the proper diagnosis cannot be reached in up to 10% of patients presenting with IBD colitis. This topic is receiving emerging attention, as medical therapies, surgical approaches and leading prognostic outcomes require more and more disease-specific strategies in IBD patients. The optimization of standard diagnostic approaches based on clinical features, biomarkers, radiology, endoscopy and histopathology appears to provide only marginal benefits. Conversely, emerging diagnostic techniques in the field of gastrointestinal endoscopy, molecular pathology, genetics, epigenetics, metabolomics and proteomics have already shown promising results. Novel advanced endoscopic imaging techniques and biomarkers can shed new light for the differential diagnosis of IBD, better reflecting diverse disease behaviors based on specific pathogenic pathways.
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Abstract
Necrotizing enterocolitis is an acute inflammatory disease, which primarily affects preterm infants, and is a leading cause of morbidity and mortality in the neonatal intensive care unit. Unfortunately, necrotizing enterocolitis can be difficult to distinguish from other diseases and clinical conditions especially during the early course of the disease. This diagnostic uncertainty is particularly relevant to clinical evaluation and medical management and potentially leads to unnecessary and extended periods of cessation of enteral feedings and prolonged courses of parenteral nutrition and antibiotics. Biomarkers are molecular indicators of a disease process, diagnosis, prognosis and can be used to monitor the effects of disease management. Historically, there has been a paucity of reliable and robust biomarkers for necrotizing enterocolitis. However, several studies have recently identified promising biomarkers. Noninvasive samples for biomarker measurement are preferred and may have certain advantages in the preterm infant. In this review article, we focus on recent exciting and promising discoveries in noninvasive biomarkers for necrotizing enterocolitis.
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Dumoulin EN, Van Biervliet S, De Vos M, Himpe J, Speeckaert MM, Delanghe JR. Faecal leukocyte esterase activity is an alternative biomarker in inflammatory bowel disease. ACTA ACUST UNITED AC 2015; 53:2003-8. [DOI: 10.1515/cclm-2015-0040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/26/2015] [Indexed: 11/15/2022]
Abstract
AbstractLeukocyte cytosolic proteins (e.g., calprotectin) are emerging biomarkers for inflammatory bowel disease. Leukocyte aryl esterase activity has been commonly used for sensitive detection of leukocytes in human body fluids such as urine. Urine test strip results are generally reported in categories. As automated strip readers allow quantitative data to be reported, sensitive quantitative detection of leukocytes in body fluids has become possible. Here, we explored the use of leukocyte esterase as a potential alternative faecal biomarker for inflammatory bowel disease.We evaluated leukocyte esterase activity in faecal extracts and compared Cobas u 411 (Roche) quantitative reflectance data with calprotectin concentration for 107 routine samples. Stability of leukocyte esterase for trypsin digestion was carried out by adding trypsin to the extract. Incubation occurred at 37 °C for 24 h or 48 h.Reproducibility of the reflectance signal was good (within-run imprecision: 6.1%; between-run imprecision: 6.2%). Results were linear in the range 10Quantitative leukocyte esterase activity of faecal extracts provides information about the leukocyte count in the gut lumen. Leukocyte esterase is a promising and affordable alternative biomarker for monitoring inflammatory bowel disease.
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Bennike T, Ayturk U, Haslauer CM, Froehlich JW, Proffen B, Barnaby O, Birkelund S, Murray MM, Warman ML, Stensballe A, Steen H. A normative study of the synovial fluid proteome from healthy porcine knee joints. J Proteome Res 2014; 13:4377-87. [PMID: 25160569 PMCID: PMC4184458 DOI: 10.1021/pr500587x] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Indexed: 12/13/2022]
Abstract
Synovial fluid in an articulating joint contains proteins derived from the blood plasma and proteins that are produced by cells within the joint tissues, such as synovium, cartilage, ligament, and meniscus. The proteome composition of healthy synovial fluid and the cellular origins of many synovial fluid components are not fully understood. Here, we present a normative proteomics study using porcine synovial fluid. Using our optimized method, we identified 267 proteins with high confidence in healthy synovial fluid. We also evaluated mRNA expression data from tissues that can contribute to the synovial fluid proteome, including synovium, cartilage, blood, and liver, to better estimate the relative contributions from these sources to specific synovial fluid components. We identified 113 proteins in healthy synovial fluid that appear to be primarily derived from plasma transudates, 37 proteins primarily derived from synovium, and 11 proteins primarily derived from cartilage. Finally, we compared the identified synovial fluid proteome to the proteome of human plasma, and we found that the two body fluids share many similarities, underlining the detected plasma derived nature of many synovial fluid components. Knowing the synovial fluid proteome of a healthy joint will help to identify mechanisms that cause joint disease and pathways involved in disease progression.
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Affiliation(s)
- Tue Bennike
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
- Department
of Health Science and Technology, Aalborg
University, Aalborg DK-9220, Denmark
| | - Ugur Ayturk
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Carla M. Haslauer
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
| | - John W. Froehlich
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
| | - Benedikt
L. Proffen
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
| | - Omar Barnaby
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
| | - Svend Birkelund
- Department
of Health Science and Technology, Aalborg
University, Aalborg DK-9220, Denmark
| | - Martha M. Murray
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
| | - Matthew L. Warman
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Allan Stensballe
- Department
of Health Science and Technology, Aalborg
University, Aalborg DK-9220, Denmark
| | - Hanno Steen
- Department of Pathology and Proteomics
Center, Department of Orthopaedic Surgery, Department of Urology, and Howard Hughes
Medical Institute, Boston Children’s
Hospital, Boston, Massachusetts 02115, United States
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Multi-omics analysis of inflammatory bowel disease. Immunol Lett 2014; 162:62-8. [PMID: 25131220 DOI: 10.1016/j.imlet.2014.07.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 06/21/2014] [Accepted: 07/29/2014] [Indexed: 12/16/2022]
Abstract
Crohn's disease and ulcerative colitis, known together as inflammatory bowel disease (IBD), are severe autoimmune disorders now causing gut inflammation and ulceration, among other symptoms, in up to 1 in 250 people worldwide. Incidence and prevalence of IBD have been increasing dramatically over the past several decades, although the causes for this increase are still unknown. IBD has both a complex genotype and a complex phenotype, and although it has received substantial attention from the medical research community over recent years, much of the etiology remains unexplained. Genome-wide association studies have identified a rich genetic signature of disease risk in patients with IBD, consisting of at least 163 genetic loci. Many of these loci contain genes directly involved in microbial handling, indicating that the genetic architecture of the disease has been driven by host-microbe interactions. In addition, systematic shifts in gut microbiome structure (enterotype) and function have been observed in patients with IBD. Furthermore, both the host genotype and enterotype are associated with aspects of the disease phenotype, including location of the disease. This provides strong evidence of interactions between host genotype and enterotype; however, there is a lack of published multi-omics data from IBD patients, and a lack of bioinformatics tools for modeling such systems. In this article we discuss, from a computational biologist's point of view, the potential benefits of and the challenges involved in designing and analyzing such multi-omics studies of IBD.
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Lee SJ, Adler B, Ekström S, Rezeli M, Végvári Á, Park JW, Malm J, Laurell T. Aptamer/ISET-MS: a new affinity-based MALDI technique for improved detection of biomarkers. Anal Chem 2014; 86:7627-34. [PMID: 25001319 DOI: 10.1021/ac501488b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
With the rapid progress in the development of new clinical biomarkers there is an unmet need of fast and sensitive multiplex analysis methods for disease specific protein monitoring. Immunoaffinity extraction integrated with matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis offers a route to rapid and sensitive protein analysis and potentially multiplex biomarker analysis. In this study, the previously reported integrated selective enrichment target (ISET)-MALDI-MS analysis was implemented with ssDNA aptamer functionalized microbeads to address the specific capturing of thrombin in complex samples. The main objective for using an aptamer as the capturing ligand was to avoid the inherently high background components, which are produced during the digestion step following the target extraction when antibodies are used. By applying a thrombin specific aptamer linked to ISET-MALDI-MS detection, a proof of concept of antibody fragment background reduction in the ISET-MALDI-MS readout is presented. Detection sensitivity was significantly increased compared to the corresponding system based on antibody-specific binding as the aptamer ligand does not induce any interfering background residues from the antibodies. The limit of detection for thrombin was 10 fmol in buffer using the aptamer/ISET-MALDI-MS configuration as confirmed by MS/MS fragmentation. The aptamer/ISET-MALDI-MS platform also displayed a limit of detection of 10 fmol for thrombin in five different human serum samples (1/10 diluted), demonstrating the applicability of the aptamer/ISET-MALDI-MS analysis in clinical samples.
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Affiliation(s)
- Su Jin Lee
- Department of Biomedical Engineering, Lund University , P.O. Box 118, SE-211 00 Lund, Sweden
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