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Xu C, Shao J. High-throughput omics technologies in inflammatory bowel disease. Clin Chim Acta 2024; 555:117828. [PMID: 38355001 DOI: 10.1016/j.cca.2024.117828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 02/06/2024] [Accepted: 02/10/2024] [Indexed: 02/16/2024]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.
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Affiliation(s)
- Chen Xu
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China
| | - Jing Shao
- Laboratory of Anti-infection and Immunity, College of Integrated Chinese and Western Medicine (College of Life Science), Anhui University of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China; Institute of Integrated Traditional Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Zhijing Building, 350 Longzihu Road, Xinzhan District, Hefei 230012, Anhui, PR China.
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2
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Lucaciu LA, Seicean R, Uifălean A, Iacobescu M, Iuga CA, Seicean A. Unveiling Distinct Proteomic Signatures in Complicated Crohn's Disease That Could Predict the Disease Course. Int J Mol Sci 2023; 24:16966. [PMID: 38069288 PMCID: PMC10707401 DOI: 10.3390/ijms242316966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation of the gastrointestinal tract often leading to complications, such as strictures and fistulae. Currently, there are no validated tools anticipating short- and long-term outcomes at an early stage. This investigation aims to elucidate variations in protein abundance across distinct CD phenotypes with the objective of uncovering potential biomarkers implicated in disease advancement. Serum samples collected from 30 CD patients and 15 healthy age-matched controls (HC) were subjected to depletion of highly abundant proteins and to a label-free mass spectrometry analysis. Twenty-four proteins were shown to be significantly different when comparing CD with HC. Of these, WD repeat-containing protein 31 (WDR31), and proteins involved in the acute inflammatory response, leucine-rich alpha-2-glycoprotein (LRG1) and serum amyloid A1 (SAA1), were more abundant in the aggressive subgroup. Against standard biomarkers, a positive correlation between SAA1 and WDR31 and C-reactive protein (CRP) was found. In this study, a unique serum biomarker panel for aggressive CD was identified, which could aid in predicting the disease course.
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Affiliation(s)
- Laura A. Lucaciu
- Department of Gastroenterology and Hepatology, “Iuliu Haţieganu” University of Medicine and Pharmacy, Croitorilor 19-21, 400162 Cluj-Napoca, Romania; (L.A.L.); (A.S.)
| | - Radu Seicean
- Department of General Surgery, First Surgical Clinic, “Iuliu Haţieganu” University of Medicine and Pharmacy, Clinicilor 3-5, 400006 Cluj-Napoca, Romania;
| | - Alina Uifălean
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 6, 400349 Cluj-Napoca, Romania; (A.U.); (C.A.I.)
| | - Maria Iacobescu
- Department of Proteomics and Metabolomics, MEDFUTURE-Research Centre for Advanced Medicine, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 4, 400349 Cluj-Napoca, Romania
| | - Cristina A. Iuga
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 6, 400349 Cluj-Napoca, Romania; (A.U.); (C.A.I.)
- Department of Proteomics and Metabolomics, MEDFUTURE-Research Centre for Advanced Medicine, “Iuliu Haţieganu” University of Medicine and Pharmacy, Louis Pasteur 4, 400349 Cluj-Napoca, Romania
| | - Andrada Seicean
- Department of Gastroenterology and Hepatology, “Iuliu Haţieganu” University of Medicine and Pharmacy, Croitorilor 19-21, 400162 Cluj-Napoca, Romania; (L.A.L.); (A.S.)
- “Prof. Dr. Octavian Fodor” Regional Institute of Gastroenterology and Hepatology, Croitorilor Street No. 19-21, 400162 Cluj-Napoca, Romania
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3
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Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
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Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
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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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Big Data in Gastroenterology Research. Int J Mol Sci 2023; 24:ijms24032458. [PMID: 36768780 PMCID: PMC9916510 DOI: 10.3390/ijms24032458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/28/2023] Open
Abstract
Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.
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Borren NZ, Ananthakrishnan AN. Precision medicine: how multiomics will shape the future of inflammatory bowel disease? Curr Opin Gastroenterol 2022; 38:382-387. [PMID: 35762697 PMCID: PMC9472771 DOI: 10.1097/mog.0000000000000847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW In this article, we provide an overview of studies examining multiomic profiling in various clinical scenarios in the management of inflammatory bowel diseases (IBDs). RECENT FINDINGS IBD arises as a result of an interplay between genetic, environmental, microbial and immunologic perturbations. The access to high throughput technology as well as the decrease in costs associated with such studies has led to a growing wealth of literature examining the utility of single or multiomic profiles in the management of IBD. Such studies have commonly examined the genome (and less frequently the epigenome), transcriptome, metabolome, proteome and the gut microbial metagenome in the context of overall IBD status or specific clinical scenarios, including the disease progression or response to treatment. The findings have provided important insight into how each of these compartments reflect underlying disease pathophysiologic processes and, in turn, can influence stratification of patients for clinical management. SUMMARY Multiomic profiling in IBD has the potential to advance the field of personalized precision medicine in the management of IBDs.
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Affiliation(s)
- Nienke Z Borren
- Department of Gastroenterology & Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
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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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Sudhakar P, Alsoud D, Wellens J, Verstockt S, Arnauts K, Verstockt B, Vermeire S. Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All. J Crohns Colitis 2022; 16:1306-1320. [PMID: 35150242 PMCID: PMC9426669 DOI: 10.1093/ecco-jcc/jjac027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease [IBD] has a multifactorial origin and originates from a complex interplay of environmental factors with the innate immune system at the intestinal epithelial interface in a genetically susceptible individual. All these factors make its aetiology intricate and largely unknown. Multi-omic datasets obtained from IBD patients are required to gain further insights into IBD biology. We here review the landscape of multi-omic data availability in IBD and identify barriers and gaps for future research. We also outline the various technical and non-technical factors that influence the utility and interpretability of multi-omic datasets and thereby the study design of any research project generating such datasets. Coordinated generation of multi-omic datasets and their systemic integration with clinical phenotypes and environmental exposures will not only enhance understanding of the fundamental mechanisms of IBD but also improve therapeutic strategies. Finally, we provide recommendations to enable and facilitate generation of multi-omic datasets.
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Affiliation(s)
- Padhmanand Sudhakar
- Corresponding author: Padhmanand Sudhakar, Translational Research in Gastrointestinal Disorders [TARGID], ON I, Herestraat 49, box 701, 3000 Leuven, Belgium. Tel.: 0032 [0]16 19 49 40;
| | - Dahham Alsoud
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Judith Wellens
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Sare Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Kaline Arnauts
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium
| | - Bram Verstockt
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Severine Vermeire
- KU Leuven Department of Chronic Diseases, Metabolism and Ageing, Translational Research Center for Gastrointestinal Disorders [TARGID], Leuven, Belgium,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
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9
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Sun XL, Qiao LC, Gong J, Wen K, Xu ZZ, Yang BL. Proteomics identifies a novel role of fibrinogen-like protein 1 in Crohn’s disease. World J Gastroenterol 2021; 27:5946-5957. [PMID: 34629811 PMCID: PMC8475002 DOI: 10.3748/wjg.v27.i35.5946] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/07/2021] [Accepted: 08/10/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Crohn’s disease (CD) is an incurable intestinal disorder with unclear etiology and pathogenesis. Currently, there is a lack of specific biomarkers and drug targets for CD in clinical practice. It is essential to identify the precise pathophysiological mechanism of CD and investigate new therapeutic targets.
AIM To explore a new biomarker and therapeutic target for CD and verify its role in the CD pathological mechanism.
METHODS Proteomics was performed to quantify the protein profile in the plasma of 20 CD patients and 20 matched healthy controls. Hub genes among the selected differentially expressed proteins (DEPs) were detected via the MCODE plugin in Cytoscape software. The expression level of one hub gene with an immunoregulatory role that interested us was verified in the inflamed intestinal tissues of 20 CD patients by immunohistochemical analysis. After that, the effects of the selected hub gene on the intestinal inflammation of CD were identified in a CD cell model by examining the levels of proinflammatory cytokines by enzyme-linked immunosorbent assays and the expression of the NF-κB signalling pathway by quantitative real-time PCR analysis and Western blot assays.
RESULTS Thirty-five DEPs were selected from 393 credible proteins identified by proteomic analysis. Among the DEPs, fibrinogen-like protein 1 (FGL1), which attracted our attention due to its function in the regulation of the immune response, had 1.722-fold higher expression in the plasma of CD patients and was identified as a hub gene by MCODE. Furthermore, the expression of FGL1 in the intestinal mucosal and epithelial tissues of CD patients was also upregulated (P < 0.05). In vitro, the mRNA levels of FGL1 and NF-κB; the protein expression levels of FGL1, IKKα, IKKβ, p-IKKα/β, p-IκBα, and p-p65; and the concentrations of the proinflammatory cytokines IL-1β, IL-6, IL-17, and TNF-α were increased (P < 0.05) after stimulation with lipopolysaccharide, which were reversed by knockdown of FGL1 with siRNA transfection (P < 0.05). Conversely, FGL1 overexpression enhanced the abovementioned results (P < 0.05).
CONCLUSION FGL1 can induce intestinal inflammation by activating the canonical NF-κB signalling pathway, and it may be considered a potential biomarker and therapeutic target for CD.
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Affiliation(s)
- Xue-Liang Sun
- First Clinical Medical College, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
- Department of Colorectal Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou 215000, Jiangsu Province, China
| | - Li-Chao Qiao
- First Clinical Medical College, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Jing Gong
- First Clinical Medical College, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
| | - Ke Wen
- Department of Colorectal Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou 215000, Jiangsu Province, China
| | - Zhi-Zhong Xu
- Department of Colorectal Surgery, Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Suzhou 215000, Jiangsu Province, China
| | - Bo-Lin Yang
- First Clinical Medical College, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, Jiangsu Province, China
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Park I, Jung J, Lee S, Park K, Ryu JW, Son MY, Cho HS, Kim DS. Characterization of terminal-ileal and colonic Crohn's disease in treatment-naïve paediatric patients based on transcriptomic profile using logistic regression. J Transl Med 2021; 19:250. [PMID: 34098982 PMCID: PMC8185924 DOI: 10.1186/s12967-021-02909-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/24/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic and idiopathic inflammatory disorder of the gastrointestinal tract and comprises ulcerative colitis (UC) and Crohn's disease (CD). Crohn's disease can affect any part of the gastrointestinal tract, but mainly the terminal ileum and colon. In the present study, we aimed to characterize terminal-ileal CD (ICD) and colonic CD (CCD) at the molecular level, which might enable a more optimized approach for the clinical care and scientific research of CD. METHODS We analyzed differentially expressed genes in samples from 23 treatment-naïve paediatric patients with CD and 25 non-IBD controls, and compared the data with previously published RNA-Seq data using multi-statistical tests and confidence intervals. We implemented functional profiling and proposed statistical methods for feature selection using a logistic regression model to identify genes that are highly associated in ICD or CCD. We also validated our final candidate genes in independent paediatric and adult cohorts. RESULTS We identified 550 genes specifically expressed in patients with CD compared with those in healthy controls (p < 0.05). Among these DEGs, 240 from patients with CCD were mainly involved in mitochondrial dysfunction, whereas 310 from patients with ICD were enriched in the ileum functions such as digestion, absorption, and metabolism. To choose the most effective gene set, we selected the most powerful genes (p-value ≤ 0.05, accuracy ≥ 0.8, and AUC ≥ 0.8) using logistic regression. Consequently, 33 genes were identified as useful for discriminating CD location; the accuracy and AUC were 0.86 and 0.83, respectively. We then validated the 33 genes with data from another independent paediatric cohort (accuracy = 0.93, AUC = 0.92) and adult cohort (accuracy = 0.88, AUC = 0.72). CONCLUSIONS In summary, we identified DEGs that are specifically expressed in CCD and ICD compared with those in healthy controls and patients with UC. Based on the feature selection analysis, 33 genes were identified as useful for discriminating CCD and ICD with high accuracy and AUC, for not only paediatric patients but also independent cohorts. We propose that our approach and the final gene set are useful for the molecular classification of patients with CD, and it could be beneficial in treatments based on disease location.
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Affiliation(s)
- Ilkyu Park
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea.,Department of Environmental Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Jaeeun Jung
- Department of Environmental Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Sugi Lee
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea.,Department of Environmental Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea
| | - Kunhyang Park
- Department of Core Facility Management Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
| | - Jea-Woon Ryu
- Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea
| | - Mi-Young Son
- Department of Stem Cell Convergence Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea.
| | - Hyun-Soo Cho
- Department of Stem Cell Convergence Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Korea.
| | - Dae-Soo Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Korea. .,Department of Environmental Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Korea.
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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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12
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Mager R, Roda G, Shalaby MK, Vetrano S. Fibrotic Strictures in Crohn's Disease: Mechanisms and Predictive Factors. Curr Drug Targets 2021; 22:241-251. [PMID: 33081672 DOI: 10.2174/1389450121666201020160803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/13/2020] [Accepted: 08/27/2020] [Indexed: 11/22/2022]
Abstract
Fibrotic strictures are one of the most severe complications of Crohn's Disease (CD). They occur in about 50% of patients at five years and in 70% at ten years of the diagnosis. The only treatment available for symptomatic fibrotic strictures is surgical resection and endoscopic dilation. Both strategies are associated with a high rate of recurrence, and with multiple surgical resections, which pose the threat of surgical morbidity and short bowel syndrome. Therefore, it is crucial to identify, early, the patients more prone to develop intestinal fibrosis to intensify follow-ups, switch to more aggressive treatments, and suggest lifestyle modifications. Scarce data are available concerning biomarkers and genetic determinants to predict which patient will develop intestinal fibrosis. Biologic or clinical markers would be useful to determine this subgroup of CD patients and to predict the onset of intestinal fibrosis and, ideally, its severity. Furthermore, the identification of environmental risk factors may suggest lifestyle changes aimed at modifying the natural course, thus decreasing the risk of complicated CD. In this review, we will critically revise clinical, environmental, genetic, and serologic factors that have been associated with a complicated CD course with a particular focus on the fibrostenosing phenotype and their possible implications as predictive factors of intestinal fibrosis.
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Affiliation(s)
- Riccardo Mager
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20090, Milan, Italy
| | - Giulia Roda
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Mohammad Khaled Shalaby
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Milan, Italy
| | - Stefania Vetrano
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20090, Milan, Italy
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13
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Brubaker DK, Kumar MP, Chiswick EL, Gregg C, Starchenko A, Vega PN, Southard-Smith AN, Simmons AJ, Scoville EA, Coburn LA, Wilson KT, Lau KS, Lauffenburger DA. An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. Sci Signal 2020; 13:13/643/eaay3258. [PMID: 32753478 DOI: 10.1126/scisignal.aay3258] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Anti-tumor necrosis factor (anti-TNF) therapy resistance is a major clinical challenge in inflammatory bowel disease (IBD), due, in part, to insufficient understanding of disease-site, protein-level mechanisms. Although proteomics data from IBD mouse models exist, data and phenotype discrepancies contribute to confounding translation from preclinical animal models of disease to clinical cohorts. We developed an approach called translatable components regression (TransComp-R) to overcome interspecies and trans-omic discrepancies between mouse models and human subjects. TransComp-R combines mouse proteomic data with patient pretreatment transcriptomic data to identify molecular features discernable in the mouse data that are predictive of patient response to therapy. Interrogating the TransComp-R models revealed activated integrin pathway signaling in patients with anti-TNF-resistant colonic Crohn's disease (cCD) and ulcerative colitis (UC). As a step toward validation, we performed single-cell RNA sequencing (scRNA-seq) on biopsies from a patient with cCD and analyzed publicly available immune cell proteomics data to characterize the immune and intestinal cell types contributing to anti-TNF resistance. We found that ITGA1 was expressed in T cells and that interactions between these cells and intestinal cell types were associated with resistance to anti-TNF therapy. We experimentally showed that the α1 integrin subunit mediated the effectiveness of anti-TNF therapy in human immune cells. Thus, TransComp-R identified an integrin signaling mechanism with potential therapeutic implications for overcoming anti-TNF therapy resistance. We suggest that TransComp-R is a generalizable framework for addressing species, molecular, and phenotypic discrepancies between model systems and patients to translationally deliver relevant biological insights.
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Affiliation(s)
- Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA.,Regenstrief Center for Healthcare Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Manu P Kumar
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Evan L Chiswick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Cecil Gregg
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alina Starchenko
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paige N Vega
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Austin N Southard-Smith
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Alan J Simmons
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Elizabeth A Scoville
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lori A Coburn
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ken S Lau
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.,Center for Mucosal Inflammation and Cancer, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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14
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An Integrated Genomic and Transcriptomic Analysis Reveals Candidates of Susceptibility Genes for Crohn's Disease in Japanese Populations. Sci Rep 2020; 10:10236. [PMID: 32581322 PMCID: PMC7314801 DOI: 10.1038/s41598-020-66951-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 06/01/2020] [Indexed: 01/01/2023] Open
Abstract
Expression quantitative trait locus (eQTL) analyses have enabled us to predict the function of disease susceptibility SNPs. However, eQTL for the effector memory T cells (TEM) located in the lamina propria mononuclear cells (LPMCs), which play an important role in Crohn's disease (CD), are not yet available. Thus, we conducted RNA sequencing and eQTL analyses of TEM cells located in the LPMCs from IBD patients (n = 20). Genome-wide association study (GWAS) was performed using genotyping data of 713 Japanese CD patients and 2,063 controls. We compared the results of GWAS and eQTL of TEM, and also performed a transcriptome-wide association study using eQTL from Genotype Tissue Expression project. By eQTL analyses of TEM, correlations of possible candidates were confirmed in 22,632 pairs and 2,463 genes. Among these candidates, 19 SNPs which showed significant correlation with tenascin-XA (TNXA) expression were significantly associated with CD in GWAS. By TWAS, TNFSF15 (FDR = 1.35e-13) in whole blood, ERV3-1 (FDR = 2.18e-2) in lymphocytes, and ZNF713 (FDR = 3.04e-2) in the sigmoid colon was significantly associated with CD. By conducting integration analyses using GWAS and eQTL data, we confirmed multiple gene transcripts are involved in the development of CD.
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15
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Ning L, Shan G, Sun Z, Lou X, Zhang F, Li S, Du H, Yu J, Chen H, Xu G. Serum proteome profiles to differentiate Crohn disease from intestinal tuberculosis and primary intestinal lymphoma: A pilot study. Medicine (Baltimore) 2019; 98:e18304. [PMID: 31852111 PMCID: PMC6922555 DOI: 10.1097/md.0000000000018304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The differential diagnosis of Crohn disease (CD) from intestinal tuberculosis (ITB) and primary intestinal lymphoma (PIL) is challenging in patients who exhibit atypical clinical characteristics. The aim of the present study was to explore the serum proteome profiles of CD, PIL and ITB and to identify their differentiations.Treatment-naïve patients with CD (n = 10), PIL (n = 10) and ITB (n = 10) were enrolled in the present study. Differentially expressed proteins (DEPs) in patient serum samples were compared between groups using tandem mass tag labeled proteomic technology. A principal component analysis (PCA) plot and volcano maps were also visualized. Functional pathway analysis was performed using Reactome. The Area under the Curve (AUC) was calculated for each DEP.A total of 818 proteins were identified through proteomic quantification. Among them, 108 DEPs were identified to be differentiated between CD and ITB, 105 proteins between CD and PIL and 55 proteins between ITB and PIL. The proteome from the three groups was distinguishable in the PCA plot. The results revealed that 19, 12, and 10 proteins (AUC ≥ 0.95) were differentially expressed between CD and PIL, CD and ITB, and PIL and ITB, respectively. Among these DEPs, tumor necrosis factor ligand superfamily member 13 was higher in CD than in ITB and PIL. Peroxiredoxin-5, T-complex protein 1 subunit Gamma, CutA, and Fibulin-5 were increased in CD and PIL when compared with ITB. The levels of fibrinogen chains were also significantly higher in patients with PIL compared with CD.The current study demonstrated that serum proteome was distinguishable among patients with CD, PIL, and ITB. The identified proteins may assist in the clinical differentiation among them.
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Affiliation(s)
- Longgui Ning
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Guodong Shan
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Zeyu Sun
- Proteomics and Metabolomics Platform, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Hangzhou, China
| | - Xinhe Lou
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Fenming Zhang
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Sha Li
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Haojie Du
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Jinghua Yu
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Hongtan Chen
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
| | - Guoqiang Xu
- Department of Gastroenterology, First Affiliated Hospital, Zhejiang University School of Medicine
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16
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Denson LA, Curran M, McGovern DPB, Koltun WA, Duerr RH, Kim SC, Sartor RB, Sylvester FA, Abraham C, de Zoeten EF, Siegel CA, Burns RM, Dobes AM, Shtraizent N, Honig G, Heller CA, Hurtado-Lorenzo A, Cho JH. Challenges in IBD Research: Precision Medicine. Inflamm Bowel Dis 2019; 25:S31-S39. [PMID: 31095701 DOI: 10.1093/ibd/izz078] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Indexed: 12/12/2022]
Abstract
Precision medicine is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and pragmatic clinical research. The Challenges in IBD Research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of a multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the precision medicine section is focused on highlighting the main gap areas that must be addressed to get closer to treatments tailored to the biological and clinical characteristics of each patient, which is the aim of precision medicine. The main gaps were identified in: 1) understanding and predicting the natural history of IBD: disease susceptibility, activity, and behavior; 2) predicting disease course and treatment response; and 3) optimizing current and developing new molecular technologies. Suggested approaches to bridge these gaps include prospective longitudinal cohort studies to identify and validate precision biomarkers for prognostication of disease course, and prediction and monitoring of treatment response. To achieve this, harmonization across studies is key as well as development of standardized methods and infrastructure. The implementation of state-of-the-art molecular technologies, systems biology and machine learning approaches for multi-omics and clinical data integration and analysis will be also fundamental. Finally, randomized biomarker-stratified trials will be critical to evaluate the clinical utility of validated signatures and biomarkers in improving patient outcomes and cost-effective care.
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Affiliation(s)
- Lee A Denson
- Cincinnati Children's Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Mark Curran
- Janssen Research and Development, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Walter A Koltun
- Department of Surgery, Division of Colon and Rectal Surgery, Pennsylvania State University, Hershey, PA, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sandra C Kim
- Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - R Balfour Sartor
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Francisco A Sylvester
- Division of Pediatric Gastroenterology, University of North Carolina at Chapel Hil, Chapel Hill, NC, USA
| | | | - Edwin F de Zoeten
- University of Colorado School of Medicine, Childrens Hospital Colorado, Aurora, CO, USA
| | - Corey A Siegel
- Dartmouth Hitchcock Medical Center, Section of Gastroenterology and Hepatology, Lebanon NH, USA
| | - Richéal M Burns
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Judy H Cho
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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17
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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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18
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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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19
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Manfredi M, Conte E, Barberis E, Buzzi A, Robotti E, Caneparo V, Cecconi D, Brandi J, Vanni E, Finocchiaro M, Astegiano M, Gariglio M, Marengo E, De Andrea M. Integrated serum proteins and fatty acids analysis for putative biomarker discovery in inflammatory bowel disease. J Proteomics 2019; 195:138-149. [DOI: 10.1016/j.jprot.2018.10.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/19/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022]
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20
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Identification of serum proteome signature of irritable bowel syndrome: Potential utility of the tool for early diagnosis and patient's stratification. J Proteomics 2018; 188:167-172. [PMID: 28757466 DOI: 10.1016/j.jprot.2017.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 02/08/2023]
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21
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Abstract
Recent advances in high-throughput laboratory technologies and bioinformatics tools are redefining how we view inflammatory bowel disease (IBD). Instead of 2 diseases, we now see a diverse set of molecular subtypes. Large-scale investigation of the genome, exome, transcriptome, proteome, metabolome, microbiome, and epigenome are providing transformative insights into the pathophysiology of IBD, with the promise of accurately predicting prognosis and targeting therapy. Understanding these tools and their application is crucial to navigating the molecular era of IBD. This review aims to help the IBD clinician understand, appreciate, and eventually incorporate this coming paradigm shift to improve the care of children with IBD.
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Shores DR, Everett AD. Children as Biomarker Orphans: Progress in the Field of Pediatric Biomarkers. J Pediatr 2018; 193:14-20.e31. [PMID: 29031860 PMCID: PMC5794519 DOI: 10.1016/j.jpeds.2017.08.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/04/2017] [Accepted: 08/30/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Darla R Shores
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD.
| | - Allen D Everett
- Division of Cardiology, Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD
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23
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Wang J, Liu Z, He X, Lian S, Liang J, Yu D, Sun D, Wu R. Selenium deficiency induces duodenal villi cell apoptosis via an oxidative stress-induced mitochondrial apoptosis pathway and an inflammatory signaling-induced death receptor pathway. Metallomics 2018; 10:1390-1400. [DOI: 10.1039/c8mt00142a] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selenium is an important nutritional trace element possessing antioxidant and anti-apoptotic properties in intestinal.
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Affiliation(s)
- Jianfa Wang
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Zhe Liu
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Xianjing He
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Shuai Lian
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Jianbin Liang
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Debin Yu
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Dongbo Sun
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
| | - Rui Wu
- College of Animal Science and Veterinary Medicine in Heilongjiang Bayi Agricultural University; Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases
- Daqing 163319
- P. R. China
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Andersson E, Bergemalm D, Kruse R, Neumann G, D’Amato M, Repsilber D, Halfvarson J. Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profiles. PLoS One 2017; 12:e0186142. [PMID: 28982144 PMCID: PMC5628935 DOI: 10.1371/journal.pone.0186142] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/26/2017] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE Genetic and immunological data indicate that inflammatory bowel disease (IBD) are characterized by specific inflammatory protein profiles. However, the serum proteome of IBD is still to be defined. We aimed to characterize the inflammatory serum protein profiles of Crohn's disease (CD) and ulcerative colitis (UC), using the novel proximity extension assay. METHODS A panel of 91 inflammatory proteins were quantified in a discovery cohort of CD (n = 54), UC patients (n = 54), and healthy controls (HCs; n = 54). We performed univariate analyses by t-test, with false discovery rate correction. A sparse partial least-squares (sPLS) approach was used to identify additional discriminative proteins. The results were validated in a replication cohort. RESULTS By univariate analysis, 17 proteins were identified with significantly different abundances in CD and HCs, and 12 when comparing UC and HCs. Additionally, 64 and 45 discriminant candidate proteins, respectively, were identified with the multivariate approach. Correspondingly, significant cross-validation error rates of 0.12 and 0.19 were observed in the discovery cohort. Only FGF-19 was identified from univariate comparisons of CD and UC, but 37 additional discriminant candidates were identified using the multivariate approach. The observed cross-validation error rate for CD vs. UC remained significant when restricting the analyses to patients in clinical remission. Using univariate comparisons, 16 of 17 CD-associated proteins and 8 of 12 UC-associated proteins were validated in the replication cohort. The area under the curve for CD and UC was 0.96 and 0.92, respectively, when the sPLS model from the discovery cohort was applied to the replication cohort. CONCLUSIONS By using the novel PEA method and a panel of inflammatory proteins, we identified proteins with significantly different quantities in CD patients and UC patients compared to HCs. Our data highlight the potential of the serum IBD proteome as a source for identification of future diagnostic biomarkers.
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Affiliation(s)
- Erik Andersson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Robert Kruse
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Gunter Neumann
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mauro D’Amato
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- BioDonostia Health Research Institute, San Sebastian, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
| | - Dirk Repsilber
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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25
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Abstract
Despite advances in our understanding of the pathophysiology underlying inflammatory bowel disease, there remains a significant need for biomarkers that can differentiate between Crohn's disease and ulcerative colitis with high sensitivity and specificity, in a cost-efficient manner. As the focus on personalized approaches to the delivery of medical treatment increases, new biomarkers are being developed to predict an individual's response to therapy and their overall disease course. In this review, we will outline many of the existing and recently developed biomarkers, detailing their role in the assessment of patients with inflammatory bowel disease. We will identify opportunities for improvement in our biomarkers, including better differentiation between the subtypes of inflammatory bowel disease. We will also discuss new targets and strategies in biomarker development, including combining modalities to create biomarker signatures to improve the ability to predict disease courses and response to therapy among individual patients.
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Incidence of Crohn's Disease and Ulcerative Colitis in Rhode Island: Report from the Ocean State Crohn's and Colitis Area Registry. Inflamm Bowel Dis 2016; 22:1456-61. [PMID: 26926039 PMCID: PMC4868763 DOI: 10.1097/mib.0000000000000745] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Studies describing the incidence of Crohn's disease (CD) and ulcerative colitis (UC) are uncommon in the United States. We sought to determine the incidence of CD and UC in the state of Rhode Island. METHODS The Ocean State Crohn's and Colitis Area Registry is a state-based inception cohort of patients newly diagnosed with inflammatory bowel disease (IBD) in Rhode Island. To confirm a diagnosis of CD, UC, or IBD unclassified (IBDU), the National Institute of Diabetes and Digestive and Kidney Diseases IBD Genetics Consortium criteria were applied in a review of medical records from gastroenterology practices located in the state of Rhode Island and adjacent to the Rhode Island border in Massachusetts and Connecticut. Using population-based data, we determined the statewide incidence of IBD in Rhode Island from 2008 to 2010. RESULTS A total of 971 Rhode Island residents were diagnosed with IBD, including 444 with CD, 486 with UC, and 41 with IBD unclassified from 2008 to 2010. The overall age- and sex-adjusted IBD incidence was 30.2 (95% confidence interval, 28.3-32.1) per 100,000 persons in this time frame with 13.9, 15.1, and 1.3 per 100,000 diagnosed with CD, UC, and IBD unclassified, respectively. Of the total incident cases in Rhode Island, 30% (n = 291) were enrolled in Ocean State Crohn's and Colitis Area Registry for follow-up. CONCLUSIONS The incidence of IBD in Rhode Island is higher than that previously reported by other population-based cohorts in the United States. Prospective follow-up of individuals enrolled in the community-based Ocean State Crohn's and Colitis Area Registry cohort is ongoing.
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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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