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Vatn SS, Lindstrøm JC, Moen AEF, Brackmann S, Tannæs TM, Olbjørn C, Bergemalm D, Keita ÅV, Gomollon F, Detlie TE, Lüders T, Kalla R, Adams A, Satsangi J, Jahnsen J, Vatn MH, Halfvarson J, Ricanek P, Nilsen H. Mucosal Gene Transcript Signatures in Treatment Naïve Inflammatory Bowel Disease: A Comparative Analysis of Disease to Symptomatic and Healthy Controls in the European IBD-Character Cohort. Clin Exp Gastroenterol 2022; 15:5-25. [PMID: 35185343 PMCID: PMC8848803 DOI: 10.2147/ceg.s343468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background Studies of the mucosal transcriptomic landscape have given new insight into the pathogenesis of inflammatory bowel disease (IBD). Recently, the predictive biomarker potential of gene expression signatures has been explored. To further investigate the mucosal gene expression in IBD, we recruited a cohort of treatment naïve patients and compared them to both symptomatic and healthy controls. Methods Altogether, 323 subjects were included: Crohn’s disease (N = 75), ulcerative colitis (N = 87) and IBD unclassified (N = 3). Additionally, there were two control groups: symptomatic controls (N = 131) and healthy controls (N = 27). Mucosal biopsies were collected during ileocolonoscopy and gene expression in inflamed and non-inflamed mucosa was explored. Gene expression profiling was performed using Agilent G3 Human Gene Expression 860K v3 One-Color microarray. We recorded information about treatment escalation to anti-TNF agents or surgery, and anti-TNF response, to explore predictive opportunities of the mucosal transcriptome. Results Gene expression profiles in symptomatic controls in whom IBD had been excluded resembled that of IBD patients and diverged from that of healthy controls. In non-inflamed Crohn’s disease and ulcerative colitis, gene set enrichment analysis revealed dysregulation of pathways involved in basic cellular biological processes. Mitochondria-associated pathways were dysregulated both in non-inflamed and inflamed Crohn’s disease and ulcerative colitis (>2.6 normalized enrichment scores <−1.8). Gene expression signatures of Crohn’s disease and ulcerative colitis did not predict time for treatment escalation (p = 0.175). No significant association was found between gene expression signatures and anti-TNF response. Conclusion Non-inflamed samples are probably superior to inflamed samples when exploring gene expression signatures in IBD and might reveal underlying mechanisms central for disease initiation. The gene expression signatures of the control groups were related to if they were symptomatic or not, which may have important implications for future study designs.
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Affiliation(s)
- Simen Svendsen Vatn
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
- Correspondence: Simen Svendsen Vatn, Akershus University Hospital, Postbox 1000, Lørenskog, 1478, Norway, Tel +47 94277594, Email
| | - Jonas Christoffer Lindstrøm
- Health Services Research Unit (HØKH), Akershus University Hospital, Lørenskog, Norway
- Department of Methods Development and Analytics, Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Aina E F Moen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Methods Development and Analytics, Division of Infectious Disease Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
| | - Stephan Brackmann
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Tone M Tannæs
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
| | - Christine Olbjørn
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pediatric and Adolescent Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Daniel Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa V Keita
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | | | - Trond Espen Detlie
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Torben Lüders
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
| | - Rahul Kalla
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, Division of Medical and Radiological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alex Adams
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, Division of Medical and Radiological Sciences, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Medical Sciences/ Experimental medicine Division, University of Oxford, Oxford, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, Division of Medical and Radiological Sciences, University of Edinburgh, Edinburgh, UK
- Translational Gastroenterology Unit, Medical Sciences/ Experimental medicine Division, University of Oxford, Oxford, UK
| | - Jørgen Jahnsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Morten H Vatn
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Petr Ricanek
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section for Clinical Molecular Biology (EpiGen), Akershus University Hospital, Lørenskog, Norway
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Kalla R, Adams AT, Bergemalm D, Vatn S, Kennedy NA, Ricanek P, Lindstrom J, Ocklind A, Hjelm F, Ventham NT, Ho GT, Petren C, Repsilber D, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjorn C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Serum proteomic profiling at diagnosis predicts clinical course, and need for intensification of treatment in inflammatory bowel disease. J Crohns Colitis 2021; 15:699-708. [PMID: 33201212 PMCID: PMC8095384 DOI: 10.1093/ecco-jcc/jjaa230] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Success in personalized medicine in complex disease is critically dependent on biomarker discovery. We profiled serum proteins using a novel proximity extension assay [PEA] to identify diagnostic and prognostic biomarkers in inflammatory bowel disease [IBD]. METHODS We conducted a prospective case-control study in an inception cohort of 552 patients [328 IBD, 224 non-IBD], profiling proteins recruited across six centres. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. Nested leave-one-out cross-validation was used to examine the performance of diagnostic and prognostic proteins. RESULTS A total of 66 serum proteins differentiated IBD from symptomatic non-IBD controls, including matrix metallopeptidase-12 [MMP-12; Holm-adjusted p = 4.1 × 10-23] and oncostatin-M [OSM; p = 3.7 × 10-16]. Nine of these proteins are associated with cis-germline variation [59 independent single nucleotide polymorphisms]. Fifteen proteins, all members of tumour necrosis factor-independent pathways including interleukin-1 (IL-1) and OSM, predicted escalation, over a median follow-up of 518 [interquartile range 224-756] days. Nested cross-validation of the entire data set allowed characterization of five-protein models [96% comprising five core proteins ITGAV, EpCAM, IL18, SLAMF7 and IL8], which define a high-risk subgroup in IBD [hazard ratio 3.90, confidence interval: 2.43-6.26], or allowed distinct two- and three-protein models for ulcerative colitis and Crohn's disease respectively. CONCLUSION We have characterized a simple oligo-protein panel that has the potential to identify IBD from symptomatic controls and to predict future disease course. Further prospective work is required to validate our findings.
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Affiliation(s)
- R Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - A T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - D Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - S Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - N A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, UK
| | - P Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | | | - F Hjelm
- Olink Proteomics, Uppsala, Sweden
| | - N T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - G T Ho
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - C Petren
- Olink Proteomics, Uppsala, Sweden
| | - D Repsilber
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - M Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - M D’Amato
- BioCruces Health Research Institute and Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- School of Biological Sciences, Monash University, Victoria, Australia
| | - F Gomollón
- HCU ‘Lozano Blesa’, IIS Aragón, Zaragoza, Spain
| | - C Olbjorn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - M H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - J Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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