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Assadsangabi A, Evans CA, Corfe BM, Lobo AJ. Exploring Predictive Biomarkers of Relapse in Ulcerative Colitis: A Proteomics Approach. Inflamm Bowel Dis 2024; 30:808-819. [PMID: 37889841 DOI: 10.1093/ibd/izad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Indexed: 10/29/2023]
Abstract
INTRODUCTION AND AIMS Risk stratification of subjects with a history of inflammatory bowel disease (IBD) into those likely to relapse and those who will remain quiescent continues to be a significant challenge. The aim of this study was to investigate whether certain proteomic signature profiles or biomarkers during remission are associated with future disease relapse in patients with ulcerative colitis (UC). METHODS Endoscopic rectal samples from patients with UC in clinical, endoscopic, and histological remission at index endoscopy were collected, as well as samplers from normal control individuals. The patients were stratified to early relapsers (ERs) if they developed clinical signs of UC flare within 6 months of index endoscopy or nonrelapsers (NRs) if there was no relapse after 36 months of follow-up. The pooled rectal samples from ERs, NRs, and control individuals were subjected to nano-liquid chromatography and tandem mass spectrometry as per standard iTRAQ (isobaric tags for relative and absolute quantitation) workflow methodology. Selected proteomics-yielded candidates were subjected to orthogonal validation via immunoblotting, in a biomarker discovery exercise. RESULTS Sixty-one patients were included, of whom 8 had clinical relapse within 6 months from the index endoscopy, and 43 patients had no clinical symptoms of relapse within the 36-month follow-up period. Ten patients who had clinical signs of relapse between 6 and 36 months were excluded. Seventeen control individuals were also included. Soluble proteomics analyses between ERs, NRs, and control individuals revealed a series of upregulated and downregulated proteins. Following orthogonal validation, upregulated TRX (P = .001) and IGHA1 (P = .001) were observed in ERs relative to NRs. CONCLUSIONS Several novel candidate tissue biomarkers have been identified in this study, which could discriminate patients with UC at risk of early relapse from those in long-term sustained remission. Our findings may pave the way for pre-emptive UC disease monitoring and therapeutic decision making.
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Affiliation(s)
- Arash Assadsangabi
- Molecular Gastroenterology Research Group, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, United Kingdom
- Gastroenterology Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom
- Gastroenterology Department, Salford Royal NHS Foundation Trust, Salford, United Kingdom
- Faculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, United Kingdom
| | - Caroline A Evans
- Molecular Gastroenterology Research Group, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, United Kingdom
- Biological and Systems Engineering Group, ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | - Bernard M Corfe
- Molecular Gastroenterology Research Group, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Alan J Lobo
- Molecular Gastroenterology Research Group, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, United Kingdom
- Gastroenterology Unit, Royal Hallamshire Hospital, Sheffield, United Kingdom
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Jagirdhar GSK, Perez JA, Perez AB, Surani S. Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease. World J Gastroenterol 2023; 29:5211-5225. [PMID: 37901450 PMCID: PMC10600960 DOI: 10.3748/wjg.v29.i36.5211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/31/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a complex disease with variability in genetic, environmental, and lifestyle factors affecting disease presentation and course. Precision medicine has the potential to play a crucial role in managing IBD by tailoring treatment plans based on the heterogeneity of clinical and temporal variability of patients. Precision medicine is a population-based approach to managing IBD by integrating environmental, genomic, epigenomic, transcriptomic, proteomic, and metabolomic factors. It is a recent and rapidly developing medicine. The widespread adoption of precision medicine worldwide has the potential to result in the early detection of diseases, optimal utilization of healthcare resources, enhanced patient outcomes, and, ultimately, improved quality of life for individuals with IBD. Though precision medicine is promising in terms of better quality of patient care, inadequacies exist in the ongoing research. There is discordance in study conduct, and data collection, utilization, interpretation, and analysis. This review aims to describe the current literature on precision medicine, its multiomics approach, and future directions for its application in IBD.
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Affiliation(s)
| | - Jose Andres Perez
- Department of Medicine, Saint Francis Health Systems, Tulsa, OK 74133, United States
| | - Andrea Belen Perez
- Department of Research, Columbia University, New York, NY 10027, United States
| | - Salim Surani
- Department of Medicine and Pharmacology, Texas A&M University, College Station, TX 77413, United States
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3
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Breaux WA, Bragg MA, M'Koma AE. Ubiquitous Colonic Ileal Metaplasia Consistent with the Diagnosis of Crohn's Colitis among Indeterminate Colitis Cohorts. MEDICAL RESEARCH ARCHIVES 2023; 11:4188. [PMID: 37854669 PMCID: PMC10584353 DOI: 10.18103/mra.v11i8.4188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Background Inadequate differentiated diagnostic features of predominantly colonic inflammatory bowel diseases i.e., ulcerative colitis and Crohn's colitis, may lead to inexact diagnosis of "indeterminate colitis". About 15% of indeterminate colitis patients are diagnosed at colonoscopy, in colonic biopsies, and/or at colectomy. Managing outcomes of indeterminate colitis, given its unpredictable clinical presentation, depends on future diagnosis of colitis, Crohn's colitis or ulcerative colitis. Objective Overview the diagnostic efficacy of ectopic colonic ileal metaplasia and human α-defens 5 (DEFA5 alias HD5) for accurate delineation of indeterminate colitis into authentic Crohn's colitis and/ or ulcerative colitis. Design We describe a targeted protein for potentially differentiating indeterminate colitis into an accurate clinical subtype diagnosis of inflammatory bowel diseases i.e., ulcerative colitis and Crohn's colitis. Patients Twenty-one patients with the clinically inexact diagnosis of indeterminate colitis were followed, reassessed and data analyzed. Main outcome measures We observed that (i) some patients had their original diagnosis changed from indeterminate colitis to either ulcerative colitis or Crohn's colitis; and (ii) human α-defensin 5 is aberrantly overexpressed in Crohn's colitis. Results Fifteen of the twenty-one (71.4%) patients with indeterminate colitis had their inconclusive diagnosis changed; nine patients changed to ulcerative colitis and six to Crohn's colitis. In human colon surgical samples, Human α-defensin-5 was significantly upregulated in Crohn's colitis. In addition, Human α-defensin 5 processing enzyme, matrix metalloptotease-7 was inversely expressed compared to Human α- Defensin 5. Limitation Due to the sequence homology of the α-defensin class of proteins, preceding efforts to raise antibodies (Abs) against DEFA5 have limitations to produce adequate specificity. The Abs used in previous assays recognizes the α-defensins, active α-defensins 5 and inactive pro- α-defensins 5. Monoclonal antibodies (mAbs) to determine specificity and sensitivity of α-defensins 5, which is diagnostic of CC disease, and NOT other α-defensins is the limitation to overcome. Conclusion It is feasible to differentiate ulcerative colitis from Crohn's colitis among patients with inexact diagnosis of indeterminate colitis using Human α-defensin 5 as a molecular biosignature delineator.
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Affiliation(s)
- William A. Breaux
- Schools of Medicine, Meharry Medical College, Division of Biomedical Sciences, Nashville, Tennessee, Unite States of America
| | - Maya A. Bragg
- Schools of Medicine, Meharry Medical College, Division of Biomedical Sciences, Nashville, Tennessee, Unite States of America
| | - Amosy E. M'Koma
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Nashville, Tennessee, Unite States of America
- Department of Surgery, Colon and Rectal Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, Unite States of America
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4
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Bragg MA, Breaux WA, M’Koma AE. Inflammatory Bowel Disease-Associated Colorectal Cancer: Translational and Transformational Risks Posed by Exogenous Free Hemoglobin Alpha Chain, A By-Product of Extravasated Erythrocyte Macrophage Erythrophagocytosis. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1254. [PMID: 37476546 PMCID: PMC10358352 DOI: 10.3390/medicina59071254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Colonic inflammatory bowel disease (IBD) encompasses ulcerative colitis (UC) and Crohn's colitis (CC). Patients with IBD are at increased risk for colitis-associated colorectal cancer (CACRC) compared to the general population. CACRC is preceded by IBD, characterized by highly heterogenous, pharmacologically incurable, pertinacious, worsening, and immune-mediated inflammatory pathologies of the colon and rectum. The molecular and immunological basis of CACRC is highly correlated with the duration and severity of inflammation, which is influenced by the exogenous free hemoglobin alpha chain (HbαC), a byproduct of infiltrating immune cells; extravasated erythrocytes; and macrophage erythrophagocytosis. The exogenous free HbαC prompts oxygen free radical-arbitrated DNA damage (DNAD) through increased cellular reactive oxygen species (ROS), which is exacerbated by decreased tissue antioxidant defenses. Mitigation of the Fenton Reaction via pharmaceutical therapy would attenuate ROS, promote apoptosis and DNAD repair, and subsequently prevent the incidence of CACRC. Three pharmaceutical options that attenuate hemoglobin toxicity include haptoglobin, deferoxamine, and flavonoids (vitamins C/E). Haptoglobin's clearance rate from plasma is inversely correlated with its size; the smaller the size, the faster the clearance. Thus, the administration of Hp1-1 may prove to be beneficial. Further, deferoxamine's hydrophilic structure limits its ability to cross cell membranes. Finally, the effectiveness of flavonoids, natural herb antioxidants, is associated with the high reactivity of hydroxyl substituents. Multiple analyses are currently underway to assess the clinical context of CACRC and outline the molecular basis of HbαC-induced ROS pathogenesis by exposing colonocytes and/or colonoids to HbαC. The molecular immunopathogenesis pathways of CACRC herein reviewed are broadly still not well understood. Therefore, this timely review outlines the molecular and immunological basis of disease pathogenesis and pharmaceutical intervention as a protective measure for CACRC.
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Affiliation(s)
| | | | - Amosy E. M’Koma
- School of Medicine, Division of Biomedical Sciences, Meharry Medical College, Nashville, TN 37208, USA; (M.A.B.); (W.A.B.)
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Fabian O, Bajer L, Drastich P, Harant K, Sticova E, Daskova N, Modos I, Tichanek F, Cahova M. A Current State of Proteomics in Adult and Pediatric Inflammatory Bowel Diseases: A Systematic Search and Review. Int J Mol Sci 2023; 24:ijms24119386. [PMID: 37298338 DOI: 10.3390/ijms24119386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are systemic immune-mediated conditions with predilection for the gastrointestinal tract and include Crohn's disease and ulcerative colitis. Despite the advances in the fields of basic and applied research, the etiopathogenesis remains largely unknown. As a result, only one third of the patients achieve endoscopic remission. A substantial portion of the patients also develop severe clinical complications or neoplasia. The need for novel biomarkers that can enhance diagnostic accuracy, more precisely reflect disease activity, and predict a complicated disease course, thus, remains high. Genomic and transcriptomic studies contributed substantially to our understanding of the immunopathological pathways involved in disease initiation and progression. However, eventual genomic alterations do not necessarily translate into the final clinical picture. Proteomics may represent a missing link between the genome, transcriptome, and phenotypical presentation of the disease. Based on the analysis of a large spectrum of proteins in tissues, it seems to be a promising method for the identification of new biomarkers. This systematic search and review summarize the current state of proteomics in human IBD. It comments on the utility of proteomics in research, describes the basic proteomic techniques, and provides an up-to-date overview of available studies in both adult and pediatric IBD.
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Affiliation(s)
- Ondrej Fabian
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology and Molecular Medicine, 3rd Faculty of Medicine, Charles University and Thomayer Hospital, 140 59 Prague, Czech Republic
| | - Lukas Bajer
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Institute of Microbiology, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Pavel Drastich
- Department of Gastroenterology and Hepatology, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Karel Harant
- Proteomics Core Facility, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
| | - Eva Sticova
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
- Department of Pathology, Royal Vinohrady Teaching Hospital, Srobarova 1150/50, 100 00 Prague, Czech Republic
| | - Nikola Daskova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Istvan Modos
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Filip Tichanek
- Department of Informatics, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
| | - Monika Cahova
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, 140 21 Prague, Czech Republic
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Lohani V, A.R A, Kundu S, Akhter MDQ, Bag S. Single-Cell Proteomics with Spatial Attributes: Tools and Techniques. ACS OMEGA 2023; 8:17499-17510. [PMID: 37251119 PMCID: PMC10210017 DOI: 10.1021/acsomega.3c00795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/12/2023] [Indexed: 05/31/2023]
Abstract
Now-a-days, the single-cell proteomics (SCP) concept is attracting interest, especially in clinical research, because it can identify the proteomic signature specific to diseased cells. This information is very essential when dealing with the progression of certain diseases, such as cancer, diabetes, Alzheimer's, etc. One of the major drawbacks of conventional destructive proteomics is that it gives an average idea about the protein expression profile in the disease condition. During the extraction of the protein from a biopsy or blood sample, proteins may come from both diseased cells and adjacent normal cells or any other cells from the disease environment. Again, SCP along with spatial attributes is utilized to learn about the heterogeneous function of a single protein. Before performing SCP, it is necessary to isolate single cells. This can be done by various techniques, including fluorescence-activated cell sorting (FACS), magnetic-activated cell sorting (MACS), laser capture microdissection (LCM), microfluidics, manual cell picking/micromanipulation, etc. Among the different approaches for proteomics, mass spectrometry-based proteomics tools are widely used for their high resolution as well as sensitivity. This Review mainly focuses on the mass spectrometry-based approaches for the study of single-cell proteomics.
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Affiliation(s)
- Vartika Lohani
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- PG Scholar, Department of Pharmacy, Banasthali
Vidyapith, Jaipur, Rajasthan 302001, India
| | - Akhiya A.R
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- PG Scholar, Department of Computational
Biology and Bioinformatics, University of
Kerala, Thiruvananthapuram, Kerala 695034, India
| | - Soumen Kundu
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - MD Quasid Akhter
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
| | - Swarnendu Bag
- CSIR
Institute of Genomics and Integrative Biology, New Delhi, Delhi 110025, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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Cecerska-Heryć E, Ronkowski B, Heryć R, Serwin N, Grygorcewicz B, Roszak M, Galant K, Dołęgowska B. Proteomic and lipidomic biomarkers in the diagnosis and progression of inflammatory bowel disease - a review. Proteomics Clin Appl 2023; 17:e2200003. [PMID: 36043901 DOI: 10.1002/prca.202200003] [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: 01/05/2022] [Revised: 07/07/2022] [Accepted: 08/19/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE There is an increasing prevalence of inflammatory bowel disease (IBD) and to date, no effective treatment has been developed and the exact etiology of this disease remains unknown. Nevertheless, a growing number of proteomic and lipidomic studies have identified certain proteins and lipids which can be used successfully in patients to improve diagnoses and monitoring of treatment. EXPERIMENTAL DESIGN We have focused on the applications of proteins and lipids for IBD diagnostics, including differentiation of Crohn's disease (CD) and ulcerative colitis (UC), treatment monitoring, monitoring of clinical state, likelihood of relapse, and their potential for novel targeted treatments. RESULTS Analysis of protein and lipid profiles can: improve the availability and use of diagnostic markers; improve understanding of the pathomechanisms of IBD, for example, several studies have implicated platelet dysfunction (PF4), autoimmune responses (granzyme B, perforin), and abnormal metabolism (arachidonic acid pathways); aid in monitoring patient health; and improve therapeutics (experimental phosphatidylcholine therapy has been shown to result in an improvement in intestinal condition). CONCLUSIONS Despite the enormous progress of proteomics and lipidomics in recent years and the development of new technologies, further research is needed to select some of the most sensitive and specific markers applicable in diagnosing and treating IBD.
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Affiliation(s)
- Elżbieta Cecerska-Heryć
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Bartosz Ronkowski
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Rafał Heryć
- Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Natalia Serwin
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Bartłomiej Grygorcewicz
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Marta Roszak
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Katarzyna Galant
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
| | - Barbara Dołęgowska
- Department of Laboratory Medicine, Pomeranian Medical University of Szczecin, Szczecin, Poland
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8
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The Current Status of Molecular Biomarkers for Inflammatory Bowel Disease. Biomedicines 2022; 10:biomedicines10071492. [PMID: 35884797 PMCID: PMC9312796 DOI: 10.3390/biomedicines10071492] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Diagnosis and prognosis of inflammatory bowel disease (IBD)-a chronic inflammation that affects the gastrointestinal tract of patients-are challenging, as most clinical symptoms are not specific to IBD, and are often seen in other inflammatory diseases, such as intestinal infections, drug-induced colitis, and monogenic diseases. To date, there is no gold-standard test for monitoring IBD. Endoscopy and imaging are essential diagnostic tools that provide information about the disease's state, location, and severity. However, the invasive nature and high cost of endoscopy make it unsuitable for frequent monitoring of disease activity in IBD patients, and even when it is possible to replace endoscopy with imaging, high cost remains a concern. Laboratory testing of blood or feces has the advantage of being non-invasive, rapid, cost-effective, and standardizable. Although the specificity and accuracy of laboratory testing alone need to be improved, it is increasingly used to monitor disease activity or to diagnose suspected IBD cases in combination with endoscopy and/or imaging. The literature survey indicates a dearth of summarization of biomarkers for IBD testing. This review introduces currently available non-invasive biomarkers of clinical importance in laboratory testing for IBD, and discusses the trends and challenges in the IBD biomarker studies.
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Baldan-Martin M, Chaparro M, Gisbert JP. Tissue Proteomic Approaches to Understand the Pathogenesis of Inflammatory Bowel Disease. Inflamm Bowel Dis 2021; 27:1184-1200. [PMID: 33529308 DOI: 10.1093/ibd/izaa352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel disease (IBD) has become a global disease encompassing a group of progressive disorders characterized by recurrent chronic inflammation of the gut with variable disease courses and complications. Despite recent advances in the knowledge of IBD pathophysiology, the elucidation of its etiopathology and progression is far from fully understood, requiring complex and multiple approaches. Therefore, limited clinical progress in diagnosis, assessment of disease activity, and optimal therapeutic regimens have been made over the past few decades. This review explores recent advances and challenges in tissue proteomics with an emphasis on biomarker discovery and better understanding of the molecular mechanisms underlying IBD pathogenesis. Future multi-omic studies are required for the comprehensive molecular characterization of disease biology in real time with a future impact on early detection, disease monitoring, and prediction of the clinical outcome.
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Affiliation(s)
- Montserrat Baldan-Martin
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
| | - Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Madrid, Spain
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Rana T, Korolkova OY, Rachakonda G, Williams AD, Hawkins AT, James SD, Sakwe AM, Hui N, Wang L, Yu C, Goodwin JS, Izban MG, Offodile RS, Washington MK, Ballard BR, Smoot DT, Shi XZ, Forbes DS, Shanker A, M’Koma AE. Linking bacterial enterotoxins and alpha defensin 5 expansion in the Crohn's colitis: A new insight into the etiopathogenetic and differentiation triggers driving colonic inflammatory bowel disease. PLoS One 2021; 16:e0246393. [PMID: 33690604 PMCID: PMC7942995 DOI: 10.1371/journal.pone.0246393] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/17/2021] [Indexed: 02/05/2023] Open
Abstract
Evidence link bacterial enterotoxins to apparent crypt-cell like cells (CCLCs), and Alpha Defensin 5 (DEFA5) expansion in the colonic mucosa of Crohn's colitis disease (CC) patients. These areas of ectopic ileal metaplasia, positive for Paneth cell (PC) markers are consistent with diagnosis of CC. Retrospectively, we: 1. Identified 21 patients with indeterminate colitis (IC) between 2000-2007 and were reevaluation their final clinical diagnosis in 2014 after a followed-up for mean 8.7±3.7 (range, 4-14) years. Their initial biopsies were analyzed by DEFA5 bioassay. 2. Differentiated ulcer-associated cell lineage (UACL) analysis by immunohistochemistry (IHC) of the CC patients, stained for Mucin 6 (MUC6) and DEFA5. 3. Treated human immortalized colonic epithelial cells (NCM460) and colonoids with pure DEFA5 on the secretion of signatures after 24hr. The control colonoids were not treated. 4. Treated colonoids with/without enterotoxins for 14 days and the spent medium were collected and determined by quantitative expression of DEFA5, CCLCs and other biologic signatures. The experiments were repeated twice. Three statistical methods were used: (i) Univariate analysis; (ii) LASSO; and (iii) Elastic net. DEFA5 bioassay discriminated CC and ulcerative colitis (UC) in a cohort of IC patients with accuracy. A fit logistic model with group CC and UC as the outcome and the DEFA5 as independent variable differentiator with a positive predictive value of 96 percent. IHC staining of CC for MUC6 and DEFA5 stained in different locations indicating that DEFA5 is not co-expressed in UACL and is therefore NOT the genesis of CC, rather a secretagogue for specific signature(s) that underlie the distinct crypt pathobiology of CC. Notably, we observed expansion of signatures after DEFA5 treatment on NCM460 and colonoids cells expressed at different times, intervals, and intensity. These factors are key stem cell niche regulators leading to DEFA5 secreting CCLCs differentiation 'the colonic ectopy ileal metaplasia formation' conspicuously of pathogenic importance in CC.
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Affiliation(s)
- Tanu Rana
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Olga Y. Korolkova
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Girish Rachakonda
- Department of Microbiology and Immunology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Amanda D. Williams
- Department of Biology, Lipscomb University, Nashville, Tennessee, United States of America
| | - Alexander T. Hawkins
- Division of General Surgery, Section of Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Samuel D. James
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Tennessee Valley Health Systems VA Medical Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Amos M. Sakwe
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Graduate Studies and Research, Nashville, Tennessee, United States of America
| | - Nian Hui
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Li Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Chang Yu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Jeffrey S. Goodwin
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Michael G. Izban
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Regina S. Offodile
- Department of Professional and Medical Education, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Billy R. Ballard
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Duane T. Smoot
- Department of Medicine, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Xuan-Zheng Shi
- Department of Medicine, University of Texas Medical Branch (UTMB) in Galveston, Galveston, Texas, United States of America
| | - Digna S. Forbes
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Anil Shanker
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Amosy E. M’Koma
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
- Division of General Surgery, Section of Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pathology, Anatomy and Cell Biology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
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Longo S, Chieppa M, Cossa LG, Spinelli CC, Greco M, Maffia M, Giudetti AM. New Insights into Inflammatory Bowel Diseases from Proteomic and Lipidomic Studies. Proteomes 2020; 8:proteomes8030018. [PMID: 32784952 PMCID: PMC7565982 DOI: 10.3390/proteomes8030018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis (UC) and Crohn's disease (CD) represent the two main forms of chronic inflammatory bowel diseases (IBD). The exact IBD etiology is not yet revealed but CD and UC are likely induced by an excessive immune response against normal constituents of the intestinal microbial flora. IBD diagnosis is based on clinical symptoms often combined with invasive and costly procedures. Thus, the need for more non-invasive markers is urgent. Several routine laboratory investigations have been explored as indicators of intestinal inflammation in IBD, including blood testing for C-reactive protein, erythrocyte sedimentation rate, and specific antibodies, in addition to stool testing for calprotectin and lactoferrin. However, none has been universally adopted, some have been well-characterized, and others hold great promise. In recent years, the technological developments within the field of mass spectrometry (MS) and bioinformatics have greatly enhanced the ability to retrieve, characterize, and analyze large amounts of data. High-throughput research allowed enhancing the understanding of the biology of IBD permitting a more accurate biomarker discovery than ever before. In this review, we summarize currently used IBD serological and stool biomarkers and how proteomics and lipidomics are contributing to the identification of IBD biomarkers.
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Affiliation(s)
- Serena Longo
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
| | - Marcello Chieppa
- National Institute of Gastroenterology “S. de Bellis”, Institute of Research, Via Turi, 27, 70013 Castellana Grotte, Italy;
| | - Luca G. Cossa
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
| | - Chiara C. Spinelli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
| | - Marco Greco
- Department of Mathematics and Physics “Ennio De Giorgi”, University of Salento, via Monteroni, 73100 Lecce, Italy;
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
- Correspondence: (M.M.); (A.M.G.)
| | - Anna M. Giudetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, via Monteroni 165, 73100 Lecce, Italy; (S.L.); (L.G.C.); (C.C.S.)
- Correspondence: (M.M.); (A.M.G.)
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12
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Klein O, Fogt F, Hollerbach S, Nebrich G, Boskamp T, Wellmann A. Classification of Inflammatory Bowel Disease from Formalin-Fixed, Paraffin-Embedded Tissue Biopsies via Imaging Mass Spectrometry. Proteomics Clin Appl 2020; 14:e1900131. [PMID: 32691971 DOI: 10.1002/prca.201900131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/25/2020] [Indexed: 01/09/2023]
Abstract
PURPOSE Discrimination between ulcerative colitis (UC) and Crohn's disease (CD) by histologic features alone can be challenging and often leads to inaccurate initial diagnoses in inflammatory bowel disease (IBD) patients. This is mostly due to an overlap of clinical and histologic features. However, exact diagnosis is not only important for patient treatment but it also has a socioeconomic impact. It is therefore important to develop and improve diagnostic tools complementing traditional histomorphological approaches. EXPERIMENTAL DESIGN In this retrospective proof-of-concept study, the utilization of MALDI imaging is explored in combination with multi-variate data analysis methods to classify formalin-fixed, paraffin-embedded (FFPE) colon biopsies from UC (87 biopsies, 14 patients), CD (71 biopsies, 14 patients), and normal colonic (21 biopsies, 14 patients) tissues. RESULTS The proposed method results in an overall balanced accuracy of 85.7% on patient and of 80.4% on sample level, thus demonstrating that the assessment of IBD from FFPE tissue specimens via MALDI imaging is feasible. CONCLUSIONS AND CLINICAL RELEVANCE The results emphasize the high potential of this method to distinguish IBD subtypes in FFPE tissue sections, which is a prerequisite for further investigations in retrospective multicenter studies, as well as for a future implementation into clinical routine.
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Affiliation(s)
- Oliver Klein
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, 13353, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Franz Fogt
- Penn Presbyterian Medical Center, Hospital of the University of Pennsylvania, 51N 39th Street, Philadelphia, PA, 19104, USA
| | - Stephan Hollerbach
- Department of Gastroenterology, AKH Celle, Siemensplatz 4, 29223, Celle, Germany
| | - Grit Nebrich
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, 13353, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353, Berlin, Germany
| | - Tobias Boskamp
- Center for Industrial Mathematics, University of Bremen, Bibliothekstr. 5, 28359, Bremen, Germany.,SCiLS, Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359, Bremen, Germany
| | - Axel Wellmann
- Institute of Pathology, Wittinger Strasse 14, 29223, Celle, Germany
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13
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Pisani LF, Moriggi M, Gelfi C, Vecchi M, Pastorelli L. Proteomic insights on the metabolism in inflammatory bowel disease. World J Gastroenterol 2020; 26:696-705. [PMID: 32116417 PMCID: PMC7039832 DOI: 10.3748/wjg.v26.i7.696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/02/2020] [Accepted: 02/09/2020] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory conditions of the gut that include Crohn's disease and ulcerative colitis. The pathogenesis of IBD is not completely unraveled, IBD are multi-factorial diseases with reported alterations in the gut microbiota, activation of different immune cell types, changes in the vascular endothelium, and alterations in the tight junctions’ structure of the colonic epithelial cells. Proteomics represents a useful tool to enhance our biological understanding and to discover biomarkers in blood and intestinal specimens. It is expected to provide reproducible and quantitative data that can support clinical assessments and help clinicians in the diagnosis and treatment of IBD. Sometimes a differential diagnosis of Crohn's disease and ulcerative colitis and the prediction of treatment response can be deducted by finding meaningful biomarkers. Although some non-invasive biomarkers have been described, none can be considered as the “gold standard” for IBD diagnosis, disease activity and therapy outcome. For these reason new studies have proposed an “IBD signature”, which consists in a panel of biomarkers used to assess IBD. The above described approach characterizes “omics” and in this review we will focus on proteomics.
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Affiliation(s)
- Laura Francesca Pisani
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Manuela Moriggi
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
| | - Cecilia Gelfi
- Department of Biomedical Science for Health, University of the Study of Milan, IRCCS Istituto Ortopedico Galeazzi, Milan 20122, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, IRCCS Ca' Granda Foundation, Policlinico Hospital, University of the Study of Milan, Milan 20122, Italy
| | - Luca Pastorelli
- Gastroenterology and Digestive Endoscopy Unit, IRCCS Policlinico San Donato, San Donato Milanese 20097, Italy
- Department of Biomedical Science for Health, University of the Study of Milan, Milan 20122, Italy
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14
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Judd AM, Gutierrez DB, Moore JL, Patterson NH, Yang J, Romer CE, Norris JL, Caprioli RM. A recommended and verified procedure for in situ tryptic digestion of formalin-fixed paraffin-embedded tissues for analysis by matrix-assisted laser desorption/ionization imaging mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:716-727. [PMID: 31254303 PMCID: PMC6711785 DOI: 10.1002/jms.4384] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/20/2019] [Accepted: 06/20/2019] [Indexed: 05/06/2023]
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a molecular imaging technology uniquely capable of untargeted measurement of proteins, lipids, and metabolites while retaining spatial information about their location in situ. This powerful combination of capabilities has the potential to bring a wealth of knowledge to the field of molecular histology. Translation of this innovative research tool into clinical laboratories requires the development of reliable sample preparation protocols for the analysis of proteins from formalin-fixed paraffin-embedded (FFPE) tissues, the standard preservation process in clinical pathology. Although ideal for stained tissue analysis by microscopy, the FFPE process cross-links, disrupts, or can remove proteins from the tissue, making analysis of the protein content challenging. To date, reported approaches differ widely in process and efficacy. This tutorial presents a strategy derived from systematic testing and optimization of key parameters, for reproducible in situ tryptic digestion of proteins in FFPE tissue and subsequent MALDI IMS analysis. The approach describes a generalized method for FFPE tissues originating from virtually any source.
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Affiliation(s)
- Audra M. Judd
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Correspondence: Dr. Richard M. Caprioli, 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA, Phone: (615) 322-4336, Fax: (615) 343-8372,
| | - Danielle B. Gutierrez
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Correspondence: Dr. Richard M. Caprioli, 9160 MRB III, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA, Phone: (615) 322-4336, Fax: (615) 343-8372,
| | - Jessica L. Moore
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
| | - Junhai Yang
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
| | - Carrie E. Romer
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
| | - Jeremy L. Norris
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Departments of Chemistry, Vanderbilt University, Nashville TN, 37235
| | - Richard M. Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, Nashville TN, 37235
- Departments of Biochemistry, Vanderbilt University, Nashville TN, 37235
- Departments of Chemistry, Vanderbilt University, Nashville TN, 37235
- Departments of Pharmacology, Vanderbilt University, Nashville TN, 37235
- Departments of Medicine, Vanderbilt University, Nashville TN, 37235
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15
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Di Narzo AF, Brodmerkel C, Telesco SE, Argmann C, Peters LA, Li K, Kidd B, Dudley J, Cho J, Schadt EE, Kasarskis A, Dobrin R, Hao K. High-Throughput Identification of the Plasma Proteomic Signature of Inflammatory Bowel Disease. J Crohns Colitis 2019; 13:462-471. [PMID: 30445421 PMCID: PMC6441306 DOI: 10.1093/ecco-jcc/jjy190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND The molecular aetiology of inflammatory bowel disease [IBD] and its two subtypes, ulcerative colitis [UC] and Crohn's disease [CD], have been carefully investigated at genome and transcriptome levels. Recent advances in high-throughput proteome quantification has enabled comprehensive large-scale plasma proteomics studies of IBD. METHODS The study used two cohorts: [1] The CERTIFI-cohort: 42 samples from the CERTIFI trial of anti-TNFα-refractory CD patients; [2] the PROgECT-UNITI-HCs cohort: 46 UC samples of the PROgECT study, 84 CD samples of the UNITI I and UNITI II studies, and 72 healthy controls recruited in Mount Sinai Hospital, New York, USA. The plasma proteome for these two cohorts was quantified using high-throughput platforms. RESULTS For the PROgECT-UNITI-HCs cohort, we measured a total of 1310 proteins. Of these, 493 proteins showed different plasma levels in IBD patients to the plasma levels in controls at 10% false discovery rate [FDR], among which 11 proteins had a fold change greater than 2. The proteins upregulated in IBD were associated with immunity functionality, whereas the proteins downregulated in IBD were associated with nutrition and metabolism. The proteomic profiles were very similar between UC and CD. In the CERTIFI cohort, 1014 proteins were measured, and it was found that the plasma protein level had little correlation with the blood or intestine transcriptomes. CONCLUSIONS We report the largest proteomics study to date on IBD and controls. A large proportion of plasma proteins are altered in IBD, which provides insights into the disease aetiology and indicates a potential for biomarker discovery.
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Affiliation(s)
- Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren A Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | | | - Brian Kidd
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joel Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, a Mount Sinai venture, Stamford, CT, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Respiratory Medicine, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, China
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16
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Gisbert JP, Chaparro M. Clinical Usefulness of Proteomics in Inflammatory Bowel Disease: A Comprehensive Review. J Crohns Colitis 2019; 13:374-384. [PMID: 30307487 DOI: 10.1093/ecco-jcc/jjy158] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The protein domain is probably the most ubiquitously affected in disease, response and recovery, and therefore proteomics holds special promise for biomarker discovery in general, and particularly in inflammatory bowel disease [IBD], i.e. ulcerative colitis and Crohn's disease. Tremendous progress has been made over the past decade in the development and refinement of proteomics technologies. These advances provide opportunities for a long-anticipated personalized medicine approach to the treatment of IBD. The present review examines the current state of IBD proteomics research and its usefulness in clinical practice. We performed a systematic bibliographic search to identify studies investigating the use of proteomics in patients with IBD, and we then summarized the current 'state of the art' in the applications of proteomic technologies in the study of IBD. In particular, in the present review we provide: [1] a brief introduction to proteomics in health and disease; [2] a review of the different stages from biomarker discovery to clinical application; and [3] a comprehensive review of the clinical usefulness and application of proteomics in IBD, including: [a] screening to differentiate IBD from healthy controls; [b] differentiating Crohn's disease from ulcerative colitis; [c] prediction of the behaviour or the IBD course; [d] prediction of IBD response to biological treatment; and [e] monitoring response to treatment. We also review the importance of the type of sample-blood vs intestinal tissue-for the study of proteomics in IBD patients. Finally, we emphasize the current limitations of proteomic studies in IBD.
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Affiliation(s)
- Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
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17
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M'Koma AE. The Multifactorial Etiopathogeneses Interplay of Inflammatory Bowel Disease: An Overview. GASTROINTESTINAL DISORDERS 2019; 1:75-105. [PMID: 37577036 PMCID: PMC10416806 DOI: 10.3390/gidisord1010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The gastrointestinal system where inflammatory bowel disease occurs is central to the immune system where the innate and the adaptive/acquired immune systems are balanced in interactions with gut microbes under homeostasis conditions. This article overviews the high-throughput research screening on multifactorial interplay between genetic risk factors, the intestinal microbiota, urbanization, modernization, Westernization, the environmental influences and immune responses in the etiopathogenesis of inflammatory bowel disease in humans. Inflammatory bowel disease is an expensive multifactorial debilitating disease that affects thousands new people annually worldwide with no known etiology or cure. The conservative therapeutics focus on the established pathology where the immune dysfunction and gut injury have already happened but do not preclude or delay the progression. Inflammatory bowel disease is evolving globally and has become a global emergence disease. It is largely known to be a disease in industrial-urbanized societies attributed to modernization and Westernized lifestyle associated with environmental factors to genetically susceptible individuals with determined failure to process certain commensal antigens. In the developing nations, increasing incidence and prevalence of inflammatory bowel disease (IBD) has been associated with rapid urbanization, modernization and Westernization of the population. In summary, there are identified multiple associations to host exposures potentiating the landscape risk hazards of inflammatory bowel disease trigger, that include: Western life-style and diet, host genetics, altered innate and/or acquired/adaptive host immune responses, early-life microbiota exposure, change in microbiome symbiotic relationship (dysbiosis/dysbacteriosis), pollution, changing hygiene status, socioeconomic status and several other environmental factors have long-standing effects/influence tolerance. The ongoing multipronged robotic studies on gut microbiota composition disparate patterns between the rural vs. urban locations may help elucidate and better understand the contribution of microbiome disciplines/ecology and evolutionary biology in potentially protecting against the development of inflammatory bowel disease.
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Affiliation(s)
- Amosy E M'Koma
- Meharry Medical College School of Medicine, Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Nashville, TN 37208, USA
- Vanderbilt University School of Medicine, Department of Surgery, Colon and Rectal Surgery, Nashville, TN 37232, USA
- The American Society of Colon and Rectal Surgeons (ASCRS), Arlington Heights, IL 60005, USA
- The American Gastroenterological Association (AGA), Bethesda, MD 20814, USA
- Vanderbilt-Ingram Cancer Center (VICC), Vanderbilt University Medical Center, Nashville, TN 37232, USA
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18
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Assadsangabi A, Evans CA, Corfe BM, Lobo A. Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives. Gastroenterol Res Pract 2019; 2019:1426954. [PMID: 30774653 PMCID: PMC6350533 DOI: 10.1155/2019/1426954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.
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Affiliation(s)
- Arash Assadsangabi
- Gastroenterology Unit, Salford Royal Hospital, Salford, UK
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology and Insigneo Institute, University of Sheffield, Sheffield, UK
| | - Caroline A. Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Bernard M. Corfe
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology and Insigneo Institute, University of Sheffield, Sheffield, UK
| | - Alan Lobo
- Gastroenterology Unit, Salford Royal Hospital, Salford, UK
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19
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Titz B, Gadaleta RM, Lo Sasso G, Elamin A, Ekroos K, Ivanov NV, Peitsch MC, Hoeng J. Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification. Int J Mol Sci 2018; 19:ijms19092775. [PMID: 30223557 PMCID: PMC6163330 DOI: 10.3390/ijms19092775] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Raffaella M Gadaleta
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
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20
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Lyons J, Brubaker DK, Ghazi PC, Baldwin KR, Edwards A, Boukhali M, Strasser SD, Suarez-Lopez L, Lin YJ, Yajnik V, Kissil JL, Haas W, Lauffenburger DA, Haigis KM. Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis. Sci Signal 2018; 11:eaan3580. [PMID: 29487189 PMCID: PMC6719711 DOI: 10.1126/scisignal.aan3580] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo. For example, the genes encoding acute-phase proteins were expressed in the liver, but the proteins were detected by MS in the colon during inflammation. We also ascertained the types of data that best described particular facets of chronic inflammation. Using gene set enrichment analysis and trans-omics coexpression network analysis, we found that each data set provided a distinct viewpoint on the molecular pathogenesis of colitis. Combining human transcriptomic data with the mouse multiomics data implicated increased p21-activated kinase (Pak) signaling as a driver of colitis. Chemical inhibition of Pak1 and Pak2 with FRAX597 suppressed active colitis in mice. These studies provide translational insights into the mechanisms contributing to colitis and identify Pak as a potential therapeutic target in IBD.
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Affiliation(s)
- Jesse Lyons
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas K Brubaker
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Phaedra C Ghazi
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Katherine R Baldwin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Pediatric Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Amanda Edwards
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Myriam Boukhali
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Samantha Dale Strasser
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lucia Suarez-Lopez
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi-Jang Lin
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Vijay Yajnik
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Joseph L Kissil
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wilhelm Haas
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kevin M Haigis
- Cancer Research Institute and Department of Medicine, Beth-Israel Deaconess Medical Center, Boston, MA 02215, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Harvard Digestive Disease Center, Harvard Medical School, Boston, MA 02115, USA
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21
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Longuespée R, Casadonte R, Schwamborn K, Reuss D, Kazdal D, Kriegsmann K, von Deimling A, Weichert W, Schirmacher P, Kriegsmann J, Kriegsmann M. Proteomics in Pathology. Proteomics 2018; 18. [DOI: 10.1002/pmic.201700361] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/16/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Rémi Longuespée
- Institute of Pathology; University Hospital Heidelberg; Heidelberg Germany
| | | | | | - David Reuss
- Department of Neuropathology, Institute of Pathology; University Hospital Heidelberg; Heidelberg Germany
- Clinical Cooperation Unit Neuropathology; German Cancer Center; Heidelberg Germany
| | - Daniel Kazdal
- Institute of Pathology; University Hospital Heidelberg; Heidelberg Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology; University Hospital Heidelberg; Heidelberg Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology; University Hospital Heidelberg; Heidelberg Germany
- Clinical Cooperation Unit Neuropathology; German Cancer Center; Heidelberg Germany
| | - Wilko Weichert
- Institute of Pathology; Technical University of Munich; Munich Germany
| | - Peter Schirmacher
- Institute of Pathology; University Hospital Heidelberg; Heidelberg Germany
| | - Jörg Kriegsmann
- Proteopath GmbH; Trier Germany
- Center for Histology; Cytology and Molecular Diagnostics; Trier Germany
| | - Mark Kriegsmann
- Institute of Pathology; University Hospital Heidelberg; Heidelberg Germany
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22
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de Souza HSP, Fiocchi C, Iliopoulos D. The IBD interactome: an integrated view of aetiology, pathogenesis and therapy. Nat Rev Gastroenterol Hepatol 2017; 14:739-749. [PMID: 28831186 DOI: 10.1038/nrgastro.2017.110] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by chronic and heterogeneous manifestations, induced by interacting environmental, genomic, microbial and immunological factors. These interactions result in an overwhelming complexity that cannot be tackled by studying the totality of each pathological component (an '-ome') in isolation without consideration of the interaction among all relevant -omes that yield an overall 'network effect'. The outcome of this effect is the 'IBD interactome', defined as a disease network in which dysregulation of individual -omes causes intestinal inflammation mediated by dysfunctional molecular modules. To define the IBD interactome, new concepts and tools are needed to implement a systems approach; an unbiased data-driven integration strategy that reveals key players of the system, pinpoints the central drivers of inflammation and enables development of targeted therapies. Powerful bioinformatics tools able to query and integrate multiple -omes are available, enabling the integration of genomic, epigenomic, transcriptomic, proteomic, metabolomic and microbiome information to build a comprehensive molecular map of IBD. This approach will enable identification of IBD molecular subtypes, correlations with clinical phenotypes and elucidation of the central hubs of the IBD interactome that will aid discovery of compounds that can specifically target the hubs that control the disease.
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Affiliation(s)
- Heitor S P de Souza
- Department of Gastroenterology & Multidisciplinary Research Laboratory, Federal University of Rio de Janeiro, Rio de Janeiro 21941-913, Brazil
| | - Claudio Fiocchi
- Department of Pathobiology, Lerner Research Institute, Department of Gastroenterology and Hepatology, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Dimitrios Iliopoulos
- Center for Systems Biomedicine, Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, USA
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23
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Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics. Mol Diagn Ther 2017; 22:11-23. [DOI: 10.1007/s40291-017-0298-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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24
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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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25
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ToF-SIMS and principal component analysis of lipids and amino acids from inflamed and dysplastic human colonic mucosa. Anal Bioanal Chem 2017; 409:6097-6111. [DOI: 10.1007/s00216-017-0546-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/17/2017] [Accepted: 07/24/2017] [Indexed: 01/14/2023]
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26
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Sotillo J, Ferreira I, Potriquet J, Laha T, Navarro S, Loukas A, Mulvenna J. Changes in protein expression after treatment with Ancylostoma caninum excretory/secretory products in a mouse model of colitis. Sci Rep 2017; 7:41883. [PMID: 28191818 PMCID: PMC5304188 DOI: 10.1038/srep41883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/03/2017] [Indexed: 12/19/2022] Open
Abstract
Different reports have highlighted the potential use of helminths and their secretions in the treatment of inflammatory bowel disease (IBD) conditions; however, no reports have investigated their effects at a proteome level. Herein, we characterise the protein expression changes that occur in lamina propria (LP) and the intestinal epithelial cells (IEC) of mice with dextran sulfate sodium (DSS)-induced colitis treated with Ancylostoma caninum excretory/secretory (ES) products using a quantitative proteomic approach. We have shown how parasite products can significantly alter the expression of proteins involved in immune responses, cell death and with an antioxidant activity. Interestingly, significant changes in the expression levels of different mucins were observed in this study. MUC13, a mucin implicated in gastrointestinal homeostasis, was upregulated in the LP of mice with DSS-induced colitis treated with ES, while MUC2, a major component of mucus, was upregulated in the IEC. In addition, A. caninum proteins have an important effect on proteins with antioxidant functions and proteins involved in intestinal homeostasis and tissue integrity and regeneration. Understanding how parasites can ameliorate IBD pathogenesis can help us design novel treatments for autoimmune diseases.
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Affiliation(s)
- Javier Sotillo
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Ivana Ferreira
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Jeremy Potriquet
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thewarach Laha
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Severine Navarro
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Alex Loukas
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,The University of Queensland, School of Biomedical Sciences, Brisbane 4072, Australia
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27
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Williams AD, Korolkova OY, Sakwe AM, Geiger TM, James SD, Muldoon RL, Herline AJ, Goodwin JS, Izban MG, Washington MK, Smoot DT, Ballard BR, Gazouli M, M'Koma AE. Human alpha defensin 5 is a candidate biomarker to delineate inflammatory bowel disease. PLoS One 2017; 12:e0179710. [PMID: 28817680 PMCID: PMC5560519 DOI: 10.1371/journal.pone.0179710] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/03/2017] [Indexed: 02/06/2023] Open
Abstract
Inability to distinguish Crohn's colitis from ulcerative colitis leads to the diagnosis of indeterminate colitis. This greatly effects medical and surgical care of the patient because treatments for the two diseases vary. Approximately 30 percent of inflammatory bowel disease patients cannot be accurately diagnosed, increasing their risk of inappropriate treatment. We sought to determine whether transcriptomic patterns could be used to develop diagnostic biomarker(s) to delineate inflammatory bowel disease more accurately. Four patients groups were assessed via whole-transcriptome microarray, qPCR, Western blot, and immunohistochemistry for differential expression of Human α-Defensin-5. In addition, immunohistochemistry for Paneth cells and Lysozyme, a Paneth cell marker, was also performed. Aberrant expression of Human α-Defensin-5 levels using transcript, Western blot, and immunohistochemistry staining levels was significantly upregulated in Crohn's colitis, p< 0.0001. Among patients with indeterminate colitis, Human α-Defensin-5 is a reliable differentiator with a positive predictive value of 96 percent. We also observed abundant ectopic crypt Paneth cells in all colectomy tissue samples of Crohn's colitis patients. In a retrospective study, we show that Human α-Defensin-5 could be used in indeterminate colitis patients to determine if they have either ulcerative colitis (low levels of Human α-Defensin-5) or Crohn's colitis (high levels of Human α-Defensin-5). Twenty of 67 patients (30 percent) who underwent restorative proctocolectomy for definitive ulcerative colitis were clinically changed to de novo Crohn's disease. These patients were profiled by Human α-Defensin-5 immunohistochemistry. All patients tested strongly positive. In addition, we observed by both hematoxylin and eosin and Lysozyme staining, a large number of ectopic Paneth cells in the colonic crypt of Crohn's colitis patient samples. Our experiments are the first to show that Human α-Defensin-5 is a potential candidate biomarker to molecularly differentiate Crohn's colitis from ulcerative colitis, to our knowledge. These data give us both a potential diagnostic marker in Human α-Defensin-5 and insight to develop future mechanistic studies to better understand crypt biology in Crohn's colitis.
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Affiliation(s)
- Amanda D. Williams
- Department of Microbiology and Immunology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
- Department of Biology, Lipscomb University, Nashville, Tennessee, United States of America
| | - Olga Y. Korolkova
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Amos M. Sakwe
- School of Graduate Studies and Research, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Timothy M. Geiger
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Samuel D. James
- Department of Pathology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology Tennessee Valley Health Systems VA Medical Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Roberta L. Muldoon
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Alan J. Herline
- Department of Surgery, Augusta University Medical Center, Augusta, Georgia, United States of America
| | - J. Shawn Goodwin
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Michael G. Izban
- Department of Pathology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Mary K. Washington
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Department of Pathology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Duane T. Smoot
- Department of Medicine, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
| | - Billy R. Ballard
- Department of Pathology, Meharry Medical College School of Medicine, Nashville General Hospital, Nashville, Tennessee, United States of America
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Amosy E. M'Koma
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee, United States of America
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
- * E-mail:
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28
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Proteome analysis of the macroscopically affected colonic mucosa of Crohn's disease and intestinal tuberculosis. Sci Rep 2016; 6:23162. [PMID: 26988818 PMCID: PMC4796817 DOI: 10.1038/srep23162] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/25/2016] [Indexed: 12/17/2022] Open
Abstract
Differentiation between intestinal tuberculosis (ITB) and Crohn’s disease (CD) is challenging in geographical regions where both these diseases are prevalent. There is a need of biomarkers for differentiation between these two disorders. Colonic biopsies from inflamed mucosa of treatment-naive patients with ITB, CD and controls were used for analysis. Protein extracted from biopsies was digested with trypsin and resulting peptides were labeled with iTRAQ reagents. The peptides were subsequently analyzed using LC-MS/MS for identification and quantification. Gene ontology annotation for proteins was analyzed in PANTHER. Validation experiments were done for six differentially expressed proteins using immunohistochemistry. 533 proteins were identified and 241 proteins were quantified from 5 sets of iTRAQ experiments. While 63 were differentially expressed in colonic mucosa of patients with CD and ITB in at least one set of iTRAQ experiment, 11 proteins were differentially expressed in more than one set of experiments. Six proteins used for validation using immunohistochemistry in a larger cohort of patients; none of them however was differentially expressed in patients with ITB and CD. There are differentially expressed proteins in tissue proteome of CD and ITB. Further experiments are required using a larger cohort of homogeneous tissue samples.
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29
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Chan PPY, Wasinger VC, Leong RW. Current application of proteomics in biomarker discovery for inflammatory bowel disease. World J Gastrointest Pathophysiol 2016; 7:27-37. [PMID: 26909226 PMCID: PMC4753187 DOI: 10.4291/wjgp.v7.i1.27] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/13/2015] [Accepted: 01/04/2016] [Indexed: 02/06/2023] Open
Abstract
Recently, the field of proteomics has rapidly expanded in its application towards clinical research with objectives ranging from elucidating disease pathogenesis to discovering clinical biomarkers. As proteins govern and/or reflect underlying cellular processes, the study of proteomics provides an attractive avenue for research as it allows for the rapid identification of protein profiles in a biological sample. Inflammatory bowel disease (IBD) encompasses several heterogeneous and chronic conditions of the gastrointestinal tract. Proteomic technology provides a powerful means of addressing major challenges in IBD today, especially for identifying biomarkers to improve its diagnosis and management. This review will examine the current state of IBD proteomics research and its use in biomarker research. Furthermore, we also discuss the challenges of translating proteomic research into clinically relevant tools. The potential application of this growing field is enormous and is likely to provide significant insights towards improving our future understanding and management of IBD.
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30
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Riaz T, Sollid LM, Olsen I, de Souza GA. Quantitative Proteomics of Gut-Derived Th1 and Th1/Th17 Clones Reveal the Presence of CD28+ NKG2D- Th1 Cytotoxic CD4+ T cells. Mol Cell Proteomics 2015; 15:1007-16. [PMID: 26637539 DOI: 10.1074/mcp.m115.050138] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 12/13/2022] Open
Abstract
T-helper cells are differentiated from CD4+ T cells and are traditionally characterized by inflammatory or immunosuppressive responses in contrast to cytotoxic CD8+ T cells. Mass-spectrometry studies on T-helper cells are rare. In this study, we aimed to identify the proteomes of human Th1 and Th1/Th17 clones derived from intestinal biopsies of Crohn's disease patients and to identify differentially expressed proteins between the two phenotypes. Crohn's disease is an inflammatory bowel disease, with predominantly Th1- and Th17-mediated response where cells of the "mixed" phenotype Th1/Th17 have also been commonly found. High-resolution mass spectrometry was used for protein identification and quantitation. In total, we identified 7401 proteins from Th1 and Th1/Th17 clones, where 334 proteins were differentially expressed. Major differences were observed in cytotoxic proteins that were overrepresented in the Th1 clones. The findings were validated by flow cytometry analyses using staining with anti-granzyme B and anti-perforin and by a degranulation assay, confirming higher cytotoxic features of Th1 compared with Th1/Th17 clones. By testing a larger panel of T-helper cell clones from seven different Crohn's disease patients, we concluded that only a subgroup of the Th1 cell clones had cytotoxic features, and these expressed the surface markers T-cell-specific surface glycoprotein CD28 and were negative for expression of natural killer group 2 member D.
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Affiliation(s)
- Tahira Riaz
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway;
| | - Ludvig Magne Sollid
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Ingrid Olsen
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway; Section for Immunology, Norwegian Veterinary Institute, Ullevaalsveien 68, 0454 Oslo, Norway
| | - Gustavo Antonio de Souza
- From the Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
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31
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Abstract
BACKGROUND Crohn's disease (CD) is a form of inflammatory bowel disease with different described behaviors, including stricture. At present, there are no laboratory studies that can differentiate stricturing CD from other phenotypes of inflammatory bowel disease. We performed a pilot study to examine differences in the proteome among patients with stricturing CD, nonstricturing CD, and ulcerative colitis. METHODS Serum samples were selected from the Ocean State Crohn's and Colitis Area Registry, an established cohort of patients with inflammatory bowel disease. Patients with CD with surgically resected stricture were matched with similar patients with CD without known stricture and with ulcerative colitis. Serum samples from each patient were digested and analyzed using liquid chromatography-mass spectrometry to characterize the proteome. Statistical analyses were performed to identify peptides and proteins that can differentiate CD with stricture. RESULTS Samples from 9 patients in each group (27 total patients) were analyzed. Baseline demographic characteristics were similar among the 3 groups. We quantified 7668 peptides and 897 proteins for analysis. Receiver operating characteristic analysis identified a subset of peptides with an area under the curve greater than 0.9, indicating greater separation potential. Partial least squares discriminant analysis was able to distinguish among the three groups with up to 70% accuracy by peptides and up to 80% accuracy by proteins. We identified the significantly different proteins and peptides and determined their function based on previously published literature. CONCLUSIONS The serum of patients with stricturing CD, nonstricturing CD, and ulcerative colitis is distinguishable through proteomic analysis. Some of the proteins that differentiate the stricturing phenotype have been implicated in complement activation, fibrinolytic pathways, and lymphocyte adhesion.
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Ballard BR, M’Koma AE. Gastrointestinal endoscopy biopsy derived proteomic patterns predict indeterminate colitis into ulcerative colitis and Crohn’s colitis. World J Gastrointest Endosc 2015; 7:670-674. [PMID: 26140094 PMCID: PMC4482826 DOI: 10.4253/wjge.v7.i7.670] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 04/24/2015] [Accepted: 05/11/2015] [Indexed: 02/05/2023] Open
Abstract
Patients with indeterminate colitis (IC) are significantly younger at diagnosis with onset of symptoms before the age of 18 years with significant morbidity in the interim. The successful care of IC is based on microscopic visual predict precision of eventual ulcerative colitis (UC) or Crohn’s colitis (CC) which is not offered in 15%-30% of inflammatory bowel disease (IBD) patients even after a combined state-of-the-art classification system of clinical, visual endoscopic, radiologic and histologic examination. These figures have not changed over the past 3 decades despite the introduction of newer diagnostic modalities. The patient outcomes after restorative proctocolectomy and ileal pouch-anal anastomosis may be painstaking if IC turns into CC. Our approach is aiming at developing a single sensitive and absolute accurate diagnostic test tool during the first clinic visit through endoscopic biopsy derived proteomic patterns. Matrix-assisted-laser desorption/ionization mass spectrometry (MS) and/or imaging MS technologies permit a histology-directed cellular test of endoscopy biopsy which identifies phenotype specific proteins, as biomarker that would assist clinicians more accurately delineate IC as being either a UC or CC or a non-IBD condition. These novel studies are underway on larger cohorts and are highly innovative with significances in differentiating a UC from CC in patients with IC and could lend mechanistic insights into IBD pathogenesis.
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33
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Korolkova OY, Myers JN, Pellom ST, Wang L, M'Koma AE. Characterization of Serum Cytokine Profile in Predominantly Colonic Inflammatory Bowel Disease to Delineate Ulcerative and Crohn's Colitides. CLINICAL MEDICINE INSIGHTS. GASTROENTEROLOGY 2015; 8:29-44. [PMID: 26078592 PMCID: PMC4459555 DOI: 10.4137/cgast.s20612] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 11/23/2014] [Accepted: 11/23/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND As accessible diagnostic approaches fail to differentiate between ulcerative colitis (UC) and Crohn’s colitis (CC) in one-third of patients with predominantly colonic inflammatory bowel disease (IBD), leading to inappropriate therapy, we aim to investigate the serum cytokine levels in these patients in search of molecular biometric markers delineating UC from CC. METHODS We measured 38 cytokines, chemokines, and growth factors using magnetic-bead-based multiplex immunoassay in 25 UC patients, 28 CC patients, and 30 controls. Our results are compared with those from a review of current literature regarding advances in serum cytokine profiles and associated challenges preventing their use for diagnostic/prognostic purposes. RESULTS Univariate analysis showed statistically significant increases of eotaxin, GRO, and TNF-α in UC patients compared to controls (Ctrl); interferon γ, interleukin (IL)-6, and IL-7 in CC group compared to Ctrl; and IL-8 in both UC and CC versus Ctrl. No cytokines were found to be different between UC and CC. A generalized linear model identified combinations of cytokines, allowing the identification of UC and CC patients, with area under the curve (AUC) = 0.936, as determined with receiver operating characteristic (ROC) analysis. CONCLUSIONS The current knowledge available about circulating cytokines in IBD is often contradictory. The development of an evidence-based tool using cytokines for diagnostic accuracy is still preliminary.
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Affiliation(s)
- Olga Y Korolkova
- Laboratory of Inflammatory Bowel Disease Research, Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Jeremy N Myers
- Laboratory of Inflammatory Bowel Disease Research, Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Samuel T Pellom
- Laboratory of Inflammatory Bowel Disease Research, Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Li Wang
- Department of Statistics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Amosy E M'Koma
- Laboratory of Inflammatory Bowel Disease Research, Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee. ; Department of General Surgery, Colon and Rectal Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee. ; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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Wang RS, Maron BA, Loscalzo J. Systems medicine: evolution of systems biology from bench to bedside. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:141-61. [PMID: 25891169 DOI: 10.1002/wsbm.1297] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/04/2015] [Accepted: 03/06/2015] [Indexed: 12/11/2022]
Abstract
High-throughput experimental techniques for generating genomes, transcriptomes, proteomes, metabolomes, and interactomes have provided unprecedented opportunities to interrogate biological systems and human diseases on a global level. Systems biology integrates the mass of heterogeneous high-throughput data and predictive computational modeling to understand biological functions as system-level properties. Most human diseases are biological states caused by multiple components of perturbed pathways and regulatory networks rather than individual failing components. Systems biology not only facilitates basic biological research but also provides new avenues through which to understand human diseases, identify diagnostic biomarkers, and develop disease treatments. At the same time, systems biology seeks to assist in drug discovery, drug optimization, drug combinations, and drug repositioning by investigating the molecular mechanisms of action of drugs at a system's level. Indeed, systems biology is evolving to systems medicine as a new discipline that aims to offer new approaches for addressing the diagnosis and treatment of major human diseases uniquely, effectively, and with personalized precision.
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Affiliation(s)
- Rui-Sheng Wang
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Bradley A Maron
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Cardiology, Veterans Affairs Boston Healthcare System, West Roxbury, MA, USA
| | - Joseph Loscalzo
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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MALDI Imaging mass spectrometry: current frontiers and perspectives in pathology research and practice. J Transl Med 2015; 95:422-31. [PMID: 25621874 DOI: 10.1038/labinvest.2014.156] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 01/14/2023] Open
Abstract
MALDI Imaging mass spectrometry has entered the field of tissue-based research by providing unique advantages for analyzing tissue specimen in an unprecedented detail. A broad spectrum of analytes ranging from proteins, peptides, protein modification over small molecules, drugs and their metabolites as well as pharmaceutical components, endogenous cell metabolites, lipids, and other analytes are made accessible by this in situ technique in tissue. Some of them were even not accessible in tissues within the histological context before. Thereby, the great advantage of MALDI Imaging is the correlation of molecular information with traditional histology by keeping the spatial localization information of the analytes after mass spectrometric measurement. This method is label-free and allows multiplex analysis of hundreds to thousands of molecules in the very same tissue section simultaneously. Imaging mass spectrometry brings a new quality of molecular data and links the expert discipline of pathology and deep molecular mass spectrometric analysis to tissue-based research. This review will focus on state-of-the-art of MALDI Imaging mass spectrometry, its recent applications by analyzing tissue specimen and the contributions in understanding the biology of disease as well as its perspectives for pathology research and practice.
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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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M'Koma AE. Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics. World J Gastrointest Surg 2014. [PMID: 25429322 DOI: 10.4240/wjgs.v6.i11.20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn's colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed.
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Affiliation(s)
- Amosy E M'Koma
- Amosy E M'Koma, Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, TN 37208-3599, United States
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M’Koma AE. Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics. World J Gastrointest Surg 2014; 6:208-219. [PMID: 25429322 PMCID: PMC4241488 DOI: 10.4240/wjgs.v6.i11.208] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 04/03/2014] [Accepted: 10/27/2014] [Indexed: 02/06/2023] Open
Abstract
Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed.
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Myers JN, Schäffer MW, Korolkova OY, Williams AD, Gangula PR, M’Koma AE. Implications of the colonic deposition of free hemoglobin-α chain: a previously unknown tissue by-product in inflammatory bowel disease. Inflamm Bowel Dis 2014; 20:1530-47. [PMID: 25078150 PMCID: PMC4134710 DOI: 10.1097/mib.0000000000000144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND We analyzed inflamed mucosal/submucosal layers of ulcerative colitis (UC = 63) and Crohn's colitis (CC = 50), and unexpectedly, we unveiled a pool of free hemoglobin alpha (Hb-α) chain. Patients with colitides have increased reactive oxidative stress (ROS), DNA oxidation products, free iron in mucosa, in preneoplastic, and in colitis-cancers and increased risks of developing colorectal cancer. All inflammatory bowel disease-related colorectal cancer lesions are found in segments with colitis. Linking this information, we investigated whether free Hb-α is key transformational stepping that increases colitis-related colorectal cancer vulnerability. METHODS UC/CC samples were profiled using matrix-assisted laser desorption/ionization mass spectrometry; protein identification was made by liquid chromatography. Diverticulitis was used as control (Ctrl). The presence of Hb(n) (n = α, β, or hemin)/Hb was validated by Western blotting and immunohistochemistry. We tested for DNA damage (DNAD) by exposing normal colonic epithelial cell line, NCM460, to 10 μM and 100 μM of Hb(n)/Hb, individually for 2, 6, and 12 hours. Quantification of Hb-α staining was done by Nikon Elements Advance Research Analysis software. ROS was measured by the production of 8-OHdG. DNAD was assessed by Comet assay. Colonic tissue homogenate antioxidants Nrf2-, CAT-, SOD-, and GPx-expressions were analyzed densitometrically/normalized by β-actin. RESULTS Immunohistochemistry of CC/UC mucosal/submucosal compartments stained strongly positive for Hb-α and significantly higher versus Ctrl. NCM460 exposed to Hb(n)/Hb exhibited steadily increasing ROS and subsequent DNAD. DNAD was higher in 10 μM than 100 μM in Hb-β/hemin the first 2 hours then plateaued followed by DNAD repair. This may be likely due to apoptosis in the later concentration. Nrf2 enzyme activities among UC, CC, and ulcerative colitis-associated colon cancer (UCAC) were observed impaired in all inflammatory bowel disease subjects. Decreased levels of Nrf2 among patients with UC versus patients with CC with active disease were insignificant as well as versus Ctrls but significantly lower in UCAC versus Ctrl. SOD was decreased in UC and UCAC and GPx in CC but statistically not significant. Comparing CC versus UC, SOD was significantly lower in CC (P < 0.05). CAT was observed increased among patients with CC/UC/UCAC and GPx in UC and UCAC versus Ctrl, respectively, and significantly increased in CC versus Ctrl (P < 0.01). CONCLUSIONS In the colitides, mucosal/submucosal tissue microenvironments demonstrated pool of free Hb-α chain. In vitro exposure of NCM460 cells to Hb(n)/Hb induced ROS and DNAD. Toxic effect of free Hb-α, in colonic epithelial cells, is therefore through production of ROS formation modulated by impairment of antioxidant effects. Targeting reduction-oxidation-sensitive pathways and transcription factors may offer options for inflammatory bowel disease-management and colitis-related cancer prevention.
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Affiliation(s)
- Jeremy N. Myers
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Michael W. Schäffer
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Olga Y. Korolkova
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Amanda D. Williams
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Pandu R. Gangula
- Department of Physiology, Meharry Medical College School of Medicine, Nashville, Tennessee
| | - Amosy E. M’Koma
- Department of Biochemistry and Cancer Biology, Meharry Medical College School of Medicine, Nashville, Tennessee
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, Tennessee
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
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Abstract
PURPOSE OF REVIEW Ulcerative colitis and Crohn's disease are the two predominant types of inflammatory bowel disease (IBD), affecting over 1.4 million individuals in the United States. IBD results from complex interactions between pathogenic components, including genetic and epigenetic factors, the immune response, and the microbiome, through an unknown sequence of events. The purpose of this review is to describe a systems biology approach to IBD as a novel and exciting methodology aiming at developing novel IBD therapeutics based on the integration of molecular and cellular 'omics' data. RECENT FINDINGS Recent evidence suggested the presence of genetic, epigenetic, transcriptomic, proteomic, and metabolomic alterations in IBD patients. Furthermore, several studies have shown that different cell types including fibroblasts, epithelial, immune, and endothelial cells together with the intestinal microbiota are involved in IBD pathogenesis. Novel computational methodologies have been developed aiming to integrate high-throughput molecular data. SUMMARY A systems biology approach could potentially identify the central regulators (hubs) in the IBD interactome and improve our understanding of the molecular mechanisms involved in IBD pathogenesis. The future IBD therapeutics should be developed on the basis of targeting the central hubs in the IBD network.
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Albalat A, Stalmach A, Bitsika V, Siwy J, Schanstra JP, Petropoulos AD, Vlahou A, Jankowski J, Persson F, Rossing P, Jaskolla TW, Mischak H, Husi H. Improving peptide relative quantification in MALDI-TOF MS for biomarker assessment. Proteomics 2014; 13:2967-75. [PMID: 23943474 DOI: 10.1002/pmic.201300100] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 06/19/2013] [Accepted: 07/13/2013] [Indexed: 12/29/2022]
Abstract
Proteomic profiling by MALDI-TOF MS presents various advantages (speed of analysis, ease of use, relatively low cost, sensitivity, tolerance against detergents and contaminants, and possibility of automation) and is being currently used in many applications (e.g. peptide/protein identification and quantification, biomarker discovery, and imaging MS). Earlier studies by many groups indicated that moderate reproducibility in relative peptide quantification is a major limitation of MALDI-TOF MS. In the present work, we examined and demonstrate a clear effect, in cases apparently random, of sample dilution in complex samples (urine) on the relative quantification of peptides by MALDI-TOF MS. Results indicate that in urine relative abundance of peptides cannot be assessed with confidence based on a single MALDI-TOF MS spectrum. To account for this issue, we developed and propose a novel method of determining the relative abundance of peptides, taking into account that peptides have individual linear quantification ranges in relation to sample dilution. We developed an algorithm that calculates the range of dilutions at which each peptide responds in a linear manner and normalizes the received peptide intensity values accordingly. This concept was successfully applied to a set of urine samples from patients diagnosed with diabetes presenting normoalbuminuria (controls) and macroalbuminuria (cases).
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Affiliation(s)
- Amaya Albalat
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, Scotland, UK
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Bennike T, Birkelund S, Stensballe A, Andersen V. Biomarkers in inflammatory bowel diseases: Current status and proteomics identification strategies. World J Gastroenterol 2014; 20:3231-3244. [PMID: 24696607 PMCID: PMC3964395 DOI: 10.3748/wjg.v20.i12.3231] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 01/13/2014] [Accepted: 02/20/2014] [Indexed: 02/06/2023] Open
Abstract
Unambiguous diagnosis of the two main forms of inflammatory bowel diseases (IBD): Ulcerative colitis (UC) and Crohn’s disease (CD), represents a challenge in the early stages of the diseases. The diagnosis may be established several years after the debut of symptoms. Hence, protein biomarkers for early and accurate diagnostic could help clinicians improve treatment of the individual patients. Moreover, the biomarkers could aid physicians to predict disease courses and in this way, identify patients in need of intensive treatment. Patients with low risk of disease flares may avoid treatment with medications with the concomitant risk of adverse events. In addition, identification of disease and course specific biomarker profiles can be used to identify biological pathways involved in the disease development and treatment. Knowledge of disease mechanisms in general can lead to improved future development of preventive and treatment strategies. Thus, the clinical use of a panel of biomarkers represents a diagnostic and prognostic tool of potentially great value. The technological development in recent years within proteomic research (determination and quantification of the complete protein content) has made the discovery of novel biomarkers feasible. Several IBD-associated protein biomarkers are known, but none have been successfully implemented in daily use to distinguish CD and UC patients. The intestinal tissue remains an obvious place to search for novel biomarkers, which blood, urine or stool later can be screened for. When considering the protein complexity encountered in intestinal biopsy-samples and the recent development within the field of mass spectrometry driven quantitative proteomics, a more thorough and accurate biomarker discovery endeavor could today be performed than ever before. In this review, we report the current status of the proteomics IBD biomarkers and discuss various emerging proteomic strategies for identifying and characterizing novel biomarkers, as well as suggesting future targets for analysis.
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M'Koma AE. Inflammatory bowel disease: an expanding global health problem. CLINICAL MEDICINE INSIGHTS. GASTROENTEROLOGY 2013; 6:33-47. [PMID: 24833941 PMCID: PMC4020403 DOI: 10.4137/cgast.s12731] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This review provides a summary of the global epidemiology of inflammatory bowel diseases (IBD). It is now clear that IBD is increasing worldwide and has become a global emergence disease. IBD, which includes Crohn’s disease (CD) and ulcerative colitis (UC), has been considered a problem in industrial-urbanized societies and attributed largely to a Westernized lifestyle and other associated environmental factors. Its incidence and prevalence in developing countries is steadily rising and has been attributed to the rapid modernization and Westernization of the population. There is a need to reconcile the most appropriate treatment for these patient populations from the perspectives of both disease presentation and cost. In the West, biological agents are the fastest-growing segment of the prescription drug market. These agents cost thousands of dollars per patient per year. The healthcare systems, and certainly the patients, in developing countries will struggle to afford such expensive treatments. The need for biological therapy will inevitably increase dramatically, and the pharmaceutical industry, healthcare providers, patient advocate groups, governments and non-governmental organizations should come to a consensus on how to handle this problem. The evidence that IBD is now affecting a much younger population presents an additional concern. Meta-analyses conducted in patients acquiring IBD at a young age also reveals a trend for their increased risk of developing colorectal cancer (CRC), since the cumulative incidence rates of CRC in IBD-patients diagnosed in childhood are higher than those observed in adults. In addition, IBD-associated CRC has a worse prognosis than sporadic CRC, even when the stage at diagnosis is taken into account. This is consistent with additional evidence that IBD negatively impacts CRC survival. A continuing increase in IBD incidence worldwide associated with childhood-onset of IBD coupled with the diseases’ longevity and an increase in oncologic transformation suggest a rising disease burden, morbidity, and healthcare costs. IBD and its associated neoplastic transformation appear inevitable, which may significantly impact pediatric gastroenterology and adult CRC care. Due to an infrastructure gap in terms of access to care between developed vs. developing nations and the uneven representation of IBD across socioeconomic strata, a plan is needed in the developing world regarding how to address this emerging problem.
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Affiliation(s)
- Amosy E M'Koma
- Laboratory of Inflammatory Bowel Disease Research, Department of Biochemistry and Cancer Biology, Meharry Medical College, Nashville TN. Departments of General Surgery, Colon and Rectal Surgery, and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville TN
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Yau Y, Leong RW, Zeng M, Wasinger VC. Proteomics and metabolomics in inflammatory bowel disease. J Gastroenterol Hepatol 2013; 28:1076-86. [PMID: 23489082 DOI: 10.1111/jgh.12193] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/01/2013] [Indexed: 12/16/2022]
Abstract
Genome-wide studies in inflammatory bowel disease (IBD) have allowed us to understand Crohn's disease and ulcerative colitis as forms of related autoinflammatory disorders that arise from a multitude of pathogenic origins. Proteomics and metabolomics are the offspring of genomics that possess unprecedented possibilities to characterize unknown pathogenic pathways. It has been about a decade since proteomics was first applied to IBD, and 5 years for metabolomics. These techniques have yielded novel and potentially important findings, but turning these results into beneficial patient outcomes remains challenging. This review recounts the history and context of clinical IBD developments before and after proteomics and metabolomics IBD in this field, discusses the challenges in consolidating high complexity data with physiological understanding, and provides an outlook on the emerging principles that will help interface the bioanalytical laboratory with IBD prognosis.
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Affiliation(s)
- Yunki Yau
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, Sydney, Australia
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Maier SK, Hahne H, Gholami AM, Balluff B, Meding S, Schoene C, Walch AK, Kuster B. Comprehensive identification of proteins from MALDI imaging. Mol Cell Proteomics 2013; 12:2901-10. [PMID: 23782541 DOI: 10.1074/mcp.m113.027599] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) is a powerful tool for the visualization of proteins in tissues and has demonstrated considerable diagnostic and prognostic value. One main challenge is that the molecular identity of such potential biomarkers mostly remains unknown. We introduce a generic method that removes this issue by systematically identifying the proteins embedded in the MALDI matrix using a combination of bottom-up and top-down proteomics. The analyses of ten human tissues lead to the identification of 1400 abundant and soluble proteins constituting the set of proteins detectable by MALDI IMS including >90% of all IMS biomarkers reported in the literature. Top-down analysis of the matrix proteome identified 124 mostly N- and C-terminally fragmented proteins indicating considerable protein processing activity in tissues. All protein identification data from this study as well as the IMS literature has been deposited into MaTisse, a new publically available database, which we anticipate will become a valuable resource for the IMS community.
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Affiliation(s)
- Stefan K Maier
- Chair for Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354 Freising, Germany
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Seeley EH, Washington MK, Caprioli RM, M'Koma AE. Proteomic patterns of colonic mucosal tissues delineate Crohn's colitis and ulcerative colitis. Proteomics Clin Appl 2013; 7:541-9. [PMID: 23382084 DOI: 10.1002/prca.201200107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 11/27/2012] [Accepted: 01/07/2013] [Indexed: 02/05/2023]
Abstract
PURPOSE Although Crohn's colitis (CC) and ulcerative colitis (UC) share several clinical features, they have different causes, mechanisms of tissue damage, and treatment options. Therefore, the accurate diagnosis is of paramount importance in terms of medical care. The distinction between CC/UC is made on the basis of clinical, radiologic, endoscopic, and pathologic interpretations but cannot be differentiated in up to 15% of inflammatory bowel disease patients. Correct management of this "indeterminate colitis" depends on the accuracy of future, and yet not known, destination diagnosis (CC/UC). EXPERIMENTAL DESIGN We have developed a proteomic methodology that has the potential to discriminate between UC/CC. The histologic layers of 62 confirmed UC/CC tissues were analyzed using MALDI-MS for proteomic profiling. RESULTS A Support Vector Machine algorithm consisting of 25 peaks was able to differentiate spectra from CC and UC with 76.9% spectral accuracy when using a leave-20%-out cross-validation. Application of the model to the entire dataset resulted in accurate classification of 19/26 CC patients and 36/36 UC patients when using a 2/3 correct cutoff. A total of 114 peaks were found to have Wilcoxin rank sum p-values of less than 0.05. CONCLUSION AND CLINICAL RELEVANCE This information may provide new avenues for the development of novel personalized therapeutic targets.
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Affiliation(s)
- Erin H Seeley
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
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Han NY, Kim EH, Choi J, Lee H, Hahm KB. Quantitative proteomic approaches in biomarker discovery of inflammatory bowel disease. J Dig Dis 2012; 13:497-503. [PMID: 22988922 DOI: 10.1111/j.1751-2980.2012.00625.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteomics offers considerable opportunities for either enhancing our biological understanding or discovering biomarkers, blood and biopsied specimen-based proteomic approaches, provide reproducible and quantitative tools that can complement clinical assessments and aid clinicians in the diagnosis and treatment of inflammatory bowel disease (IBD). Sometimes a differential diagnosis of Crohn's disease (CD) and ulcerative colitis (UC) and the prediction of treatment response can be deduced by finding meaningful biomarkers, for which the central platform for proteomics is tandem mass spectrometry (MS/MS). A range of workflows are available for protein (or peptide) separation prior to MS/MS as well as bioinformatics analysis to achieve protein identification, for which two-dimensional electrophoresis (2-DE) and subsequent mass spectrometry (MS), liquid chromatography-MS, difference gel electrophoresis following 2-DE, isobaric tags for relative and absolute quantification (iTRAQ), stable isotope labeling by amino acids and label-free quantification are under development. In this article, the current status and perspective of these advanced proteomic technologies are introduced, with examples of recent biomarkers focused on the diagnosis, treatment response, prognosis of IBD, and even colitis-associated carcinogenesis in both animal models and human patients.
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Affiliation(s)
- Na-Young Han
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, Korea
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48
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Abstract
Inflammatory bowel diseases (IBD) including ulcerative colitis and Crohn's disease are chronically relapsing, immune-mediated disorders of the gastrointestinal tract. A major challenge in the treatment of IBD is the heterogenous nature of these pathologies. Both, ulcerative colitis and Crohn's disease are of multifactorial etiology and feature a complex interaction of host genetic susceptibility and environmental factors such as diet and gut microbiota. Genome-wide association studies identified disease-relevant single-nucleotide polymorphisms in approximately 100 genes, but at the same time twin studies also clearly indicated a strong environmental impact in disease development. However, attempts to link dietary factors to the risk of developing IBD, based on epidemiological observations showed controversial outcomes. Yet, emerging high-throughput technologies implying complete biological systems might allow taking nutrient-gene interactions into account for a better classification of patient subsets in the future. In this context, 2 new scientific fields, "nutrigenetics" and "nutrigenomics" have been established. "Nutrigenetics," studying the effect of genetic variations on nutrient-gene interactions and "Nutrigenomics," describing the impact of nutrition on physiology and health status on the level of gene transcription, protein expression, and metabolism. It is hoped that the integration of both research areas will promote the understanding of the complex gene-environment interaction in IBD etiology and in the long-term will lead to personalized nutrition for disease prevention and treatment. This review briefly summarizes data on the impact of nutrients on intestinal inflammation, highlights nutrient-gene interactions, and addresses the potential of applying "omic" technologies in the context of IBD.
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Balluff B, Rauser S, Ebert MP, Siveke JT, Höfler H, Walch A. Direct molecular tissue analysis by MALDI imaging mass spectrometry in the field of gastrointestinal disease. Gastroenterology 2012; 143:544-549.e2. [PMID: 22820311 DOI: 10.1053/j.gastro.2012.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Benjamin Balluff
- Institute of Pathology, Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Sandra Rauser
- Institute of Pathology, Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias P Ebert
- Department of Medicine II, Universitätsklinikum Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jens T Siveke
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
| | - Heinz Höfler
- Institute of Pathology, Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Pathology, Technische Universität München, Munich, Germany
| | - Axel Walch
- Institute of Pathology, Research Unit Analytical Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
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Scaeffer MW, M'Koma AE, Smith JC, Ballard BR, Erin SH, Washington MK, Norris JL, Schey KL, Caprioli RM, Adunyah SE. Abstract B68: Colorectal Cancer in the Setting of Inflammatory Bowel Disease: Role of Hemoglobin. Clin Cancer Res 2012. [DOI: 10.1158/1078-0432.mechres-b68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal carcinoma (CRC) is a serious complication of inflammatory bowel disease (IBD) and accounts for approximately 15% of all IBD-associated deaths. The likelihood of IBD-related carcinoma is greater than that of sporadic CRC. Over one half are diagnosed at stage III or IV when cancer cells have already invaded surrounding tissues and most conventional therapeutics are limited in their success. Therefore the early detection of cancer, which is difficult in IBD, is crucial for its ultimate control and prevention. While mining the colonic mucosal and submucosal layers for biomarkers that differentiate ulcerative colitis (UC) from Crohn's colitis (CC) using Matrix-assisted laser desorption/ionization (MALDI) profiling, we found a signal at m/z 5045 to be more intense in UC. Liquid chromatography–mass spectrometry (LC-MS/MS) analysis allowed identification of this signal as triply charged hemoglobin alpha chain.
Macrophages are highly versatile phagocytes active in multiple roles in the immune system and key players in the inflammatory response. Their presence within the inflammatory microenvironment, in some cases, has been proven to increase transformation, angiogenesis, and immunosuppression. In hemorrhagic situations (as in UC), macrophages engulf erythrocytes that are outside the vascular bed and as a result free hemoglobin is released. Hemoglobin induces DNA damage in human colonic cells and is genotoxic. The potential carcinogenic effects of hemoglobin were documented when it was shown that hemoglobin increases the number of aberrant crypt foci in colon mucosa. In the colon, free hemoglobin is expected to increase the production of reactive oxygen (O2) species (ROS) from peroxides via the Fenton reaction, which may be the cause of cellular toxicity and eventually pro-mutagenic lesions. Intracellular reactions with active O2 can result in the initiation and progression of carcinogenesis by induction of gene mutations, chromosomal damage and cytotoxic effects.
We hypothesize that elevated expression of mucosal free hemoglobin would be associated with an increased risk of CRC. To validate this hypothesis will require investigating whether hemoglobin could be classified as a proliferative or transforming agent for colon cancer cells by causing reactive oxygen species release and subsequent DNA damage. For this purpose, we will assess the cellular viability of normal colonic cell-lines, NCM 356 and NCM 460. These cell-lines will be treated with hemoglobin at different concentrations to determine the changes in levels of ROS. ROS production will be measured using C-400 staining assay and further analysis will be carried out using FACS. Additionally, we will also examine the potential cytotoxicity of hemoglobin.
Supported: MMC-VICC Cancer Partnership Grant#: 3U54CA091408-09S 1; MeTRC grant#: 5U54RR026140-03, and Vanderbilt SPORE in GI Cancer Grant#: P50CA095103.
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Affiliation(s)
- Michael W. Scaeffer
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Amosy E. M'Koma
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Joan C. Smith
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Billy R. Ballard
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Seeley H. Erin
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Mary K. Washington
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Jeremy L. Norris
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Kevin L. Schey
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Richard M. Caprioli
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
| | - Samuel E. Adunyah
- 1Meharry Medical College School of Medicine, Nashville, TN, 2Vanderbilt University Medical School of Medicine, Nashville, TN
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