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Hu S, Bourgonje AR, Gacesa R, Jansen BH, Björk JR, Bangma A, Hidding IJ, van Dullemen HM, Visschedijk MC, Faber KN, Dijkstra G, Harmsen HJM, Festen EAM, Vich Vila A, Spekhorst LM, Weersma RK. Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease. Nat Commun 2024; 15:1470. [PMID: 38368394 PMCID: PMC10874382 DOI: 10.1038/s41467-024-45855-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/05/2024] [Indexed: 02/19/2024] Open
Abstract
Disrupted host-microbe interactions at the mucosal level are key to the pathophysiology of IBD. This study aimed to comprehensively examine crosstalk between mucosal gene expression and microbiota in patients with IBD. To study tissue-specific interactions, we perform transcriptomic (RNA-seq) and microbial (16S-rRNA-seq) profiling of 697 intestinal biopsies (645 derived from 335 patients with IBD and 52 from 16 non-IBD controls). Mucosal gene expression patterns in IBD are mainly determined by tissue location and inflammation, whereas the mucosal microbiota composition shows a high degree of individual specificity. Analysis of transcript-bacteria interactions identifies six distinct groups of inflammation-related pathways that are associated with intestinal microbiota (adjusted P < 0.05). An increased abundance of Bifidobacterium is associated with higher expression of genes involved in fatty acid metabolism, while Bacteroides correlates with increased metallothionein signaling. In patients with fibrostenosis, a transcriptional network dominated by immunoregulatory genes is associated with Lachnoclostridium bacteria in non-stenotic tissue (adjusted P < 0.05), while being absent in CD without fibrostenosis. In patients using TNF-α-antagonists, a transcriptional network dominated by fatty acid metabolism genes is linked to Ruminococcaceae (adjusted P < 0.05). Mucosal microbiota composition correlates with enrichment of intestinal epithelial cells, macrophages, and NK-cells. Overall, these data demonstrate the presence of context-specific mucosal host-microbe interactions in IBD, revealing significantly altered inflammation-associated gene-taxa modules, particularly in patients with fibrostenotic CD and patients using TNF-α-antagonists. This study provides compelling insights into host-microbe interactions that may guide microbiota-directed precision medicine and fuels the rationale for microbiota-targeted therapeutics as a strategy to alter disease course in IBD.
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Affiliation(s)
- Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Institute of Precision Medicine, the First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Bernadien H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Amber Bangma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iwan J Hidding
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, Medisch Spectrum Twente, Enschede, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Karmi N, Bangma A, Spekhorst LM, van Dullemen HM, Visschedijk MC, Dijkstra G, Weersma RK, Voskuil MD, Festen EAM. Polygenetic risk scores do not add predictive power to clinical models for response to anti-TNFα therapy in inflammatory bowel disease. PLoS One 2021; 16:e0256860. [PMID: 34534227 PMCID: PMC8448323 DOI: 10.1371/journal.pone.0256860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Anti-tumour necrosis factor alpha (TNFα) therapy is widely used in the management of Crohn’s disease (CD) and ulcerative colitis (UC). However, up to a third of patients do not respond to induction therapy and another third of patients lose response over time. To aid patient stratification, polygenetic risk scores have been identified as predictors of response to anti-TNFα therapy. We aimed to replicate the association between polygenetic risk scores and response to anti-TNFα therapy in an independent cohort of patients, to establish its clinical validity. Materials and methods Primary non-response, primary response, durable response and loss of response to anti-TNFα therapy was retrospectively assessed for each patient using stringent definitions. Genome wide genotyping was performed and previously described polygenetic risk scores for primary non-response and durable response were calculated. We compared polygenetic risk scores between patients with primary response and primary non-response, and between patients with durable response and loss of response, using separate analyses for CD and UC. Results Out of 334 patients with CD, 15 (4%) patients met criteria for primary non-response, 221 (66%) for primary response, 115 (34%) for durable response and 35 (10%) for loss of response. Out of 112 patients with UC, 12 (11%) met criteria for primary non-response, 68 (61%) for primary response, 19 (17%) for durable response and 20 (18%) for loss of response. No significant differences in polygenetic risk scores were found between primary non-responders and primary responders, and between durable responders and loss of responders. Conclusions We could not replicate the previously reported association between polygenetic risk scores and response to anti-TNFα therapy in an independent cohort of patients with CD or UC. Currently, there is insufficient evidence to use polygenetic risk scores to predict response to anti-TNFα therapy in patients with IBD.
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Affiliation(s)
- Naomi Karmi
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Amber Bangma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lieke M. Spekhorst
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hendrik M. van Dullemen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marijn C. Visschedijk
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michiel D. Voskuil
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Eleonora A. M. Festen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- * E-mail:
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3
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Bourgonje AR, Hu S, Spekhorst LM, Zhernakova DV, Vich Vila A, Li Y, Voskuil MD, van Berkel LA, Bley Folly B, Charrout M, Mahfouz A, Reinders MJT, van Heck JIP, Joosten LAB, Visschedijk MC, van Dullemen HM, Faber KN, Samsom JN, Festen EAM, Dijkstra G, Weersma RK. The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease. J Crohns Colitis 2021; 16:414-429. [PMID: 34491321 PMCID: PMC8919819 DOI: 10.1093/ecco-jcc/jjab157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
BACKGROUND AND AIMS Protein profiling in patients with inflammatory bowel diseases [IBD] for diagnostic and therapeutic purposes is underexplored. This study analysed the association between phenotype, genotype, and the plasma proteome in IBD. METHODS A total of 92 inflammation-related proteins were quantified in plasma of 1028 patients with IBD (567 Crohn's disease [CD]; 461 ulcerative colitis [UC]) and 148 healthy individuals to assess protein-phenotype associations. Corresponding whole-exome sequencing and global screening array data of 919 patients with IBD were included to analyse the effect of genetics on protein levels (protein quantitative trait loci [pQTL] analysis). Intestinal mucosal RNA sequencing and faecal metagenomic data were used for complementary analyses. RESULTS Thirty-two proteins were differentially abundant between IBD and healthy individuals, of which 22 proteins were independent of active inflammation; 69 proteins were associated with 15 demographic and clinical factors. Fibroblast growth factor-19 levels were decreased in CD patients with ileal disease or a history of ileocecal resection. Thirteen novel cis-pQTLs were identified and 10 replicated from previous studies. One trans-pQTL of the fucosyltransferase 2 [FUT2] gene [rs602662] and two independent cis-pQTLs of C-C motif chemokine 25 [CCL25] affected plasma CCL25 levels. Intestinal gene expression data revealed an overlapping cis-expression [e]QTL-variant [rs3745387] of the CCL25 gene. The FUT2 rs602662 trans-pQTL was associated with reduced abundances of faecal butyrate-producing bacteria. CONCLUSIONS This study shows that genotype and multiple disease phenotypes strongly associate with the plasma inflammatory proteome in IBD, and identifies disease-associated pathways that may help to improve disease management in the future.
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Affiliation(s)
| | | | | | - Daria V Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands,Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St Petersburg, Russia
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Yanni Li
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Lisette A van Berkel
- Department of Pediatrics, Division of Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Brenda Bley Folly
- Department of Pediatrics, Division of Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mohammed Charrout
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands,Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Julia I P van Heck
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Janneke N Samsom
- Department of Pediatrics, Division of Gastroenterology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands,Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Corresponding author: Prof. Rinse K. Weersma, MD, PhD, Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, P.O. Box 30.001, 9700 RB Groningen, The Netherlands. Tel.: +31 50 361 26 20; fax: +31 50 361 93 06;
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4
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Voskuil MD, Spekhorst LM, van der Sloot KWJ, Jansen BH, Dijkstra G, van der Woude CJ, Hoentjen F, Pierik MJ, van der Meulen AE, de Boer NKH, Löwenberg M, Oldenburg B, Festen EAM, Weersma RK. Genetic Risk Scores Identify Genetic Aetiology of Inflammatory Bowel Disease Phenotypes. J Crohns Colitis 2020; 15:930-937. [PMID: 33152062 PMCID: PMC8218708 DOI: 10.1093/ecco-jcc/jjaa223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Inflammatory bowel disease [IBD] phenotypes are very heterogeneous between patients, and current clinical and molecular classifications do not accurately predict the course that IBD will take over time. Genetic determinants of disease phenotypes remain largely unknown but could aid drug development and allow for personalised management. We used genetic risk scores [GRS] to disentangle the genetic contributions to IBD phenotypes. METHODS Clinical characteristics and imputed genome-wide genetic array data of patients with IBD were obtained from two independent cohorts [cohort A, n = 1097; cohort B, n = 2156]. Genetic risk scoring [GRS] was used to assess genetic aetiology shared across traits and IBD phenotypes. Significant GRS-phenotype (false-discovery rate [FDR] corrected p <0.05) associations identified in cohort A were put forward for replication in cohort B. RESULTS Crohn's disease [CD] GRS were associated with fibrostenotic CD [R2 = 7.4%, FDR = 0.02] and ileocaecal resection [R2 = 4.1%, FDR = 1.6E-03], and this remained significant after correcting for previously identified clinical and genetic risk factors. Ulcerative colitis [UC] GRS [R2 = 7.1%, FDR = 0.02] and primary sclerosing cholangitis [PSC] GRS [R2 = 3.6%, FDR = 0.03] were associated with colonic CD, and these two associations were largely driven by genetic variation in MHC. We also observed pleiotropy between PSC genetic risk and smoking behaviour [R2 = 1.7%, FDR = 0.04]. CONCLUSIONS Patients with a higher genetic burden of CD are more likely to develop fibrostenotic disease and undergo ileocaecal resection, whereas colonic CD shares genetic aetiology with PSC and UC that is largely driven by variation in MHC. These results further our understanding of specific IBD phenotypes.
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Affiliation(s)
- M D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - L M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - K W J van der Sloot
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands,Department of Epidemiology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - B H Jansen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - G Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C J van der Woude
- Department of Gastroenterology and Hepatology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - F Hoentjen
- Department of Gastroenterology and Hepatology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - M J Pierik
- Department of Gastroenterology and Hepatology, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - A E van der Meulen
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - N K H de Boer
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Vrije Universiteit Amsterdam, AG&M Research Institute, Amsterdam, The Netherlands
| | - M Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - B Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands,Corresponding author: Prof. Rinse K. Weersma, MD PhD, Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, Hanzeplein 1, 9700 RB Groningen, The Netherlands.
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5
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Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vila AV, Collij V, Spekhorst LM, Van der Sloot KWJ, Peters V, Van Dullemen HM, Visschedijk MC, Festen EAM, Swertz MA, Dijkstra G, Weersma RK. Correction to: The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. BMC Gastroenterol 2019; 19:44. [PMID: 30917794 PMCID: PMC6436211 DOI: 10.1186/s12876-019-0938-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 11/10/2022] Open
Affiliation(s)
- Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - K J Van der Velde
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - A Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - V Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - L M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - K W J Van der Sloot
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands
| | - V Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands
| | - H M Van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands
| | - M C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands
| | - E A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M A Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - G Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.
| | - R K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB, Groningen, the Netherlands.
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6
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Severs M, Spekhorst LM, Mangen MJJ, Dijkstra G, Löwenberg M, Hoentjen F, van der Meulen-de Jong AE, Pierik M, Ponsioen CY, Bouma G, van der Woude JC, van der Valk ME, Romberg-Camps MJL, Clemens CHM, van de Meeberg P, Mahmmod N, Jansen J, Jharap B, Weersma RK, Oldenburg B, Festen EAM, Fidder HH. Sex-Related Differences in Patients With Inflammatory Bowel Disease: Results of 2 Prospective Cohort Studies. Inflamm Bowel Dis 2018; 24:1298-1306. [PMID: 29688413 DOI: 10.1093/ibd/izy004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The understanding of gender differences in inflammatory bowel disease (IBD) patients is an important step towards tailored treatment for the individual patient. The aim of this study was to compare disease phenotype, clinical manifestations, disease activity, and healthcare utilization between men and women with Crohn's disease (CD) and ulcerative colitis (UC). METHODS Two multicenter observational cohort studies with a prospective design were used to explore the differences between men and women regarding demographic and phenotypic characteristics and healthcare utilization. Detailed data on IBD-phenotype was mainly available from the Dutch IBD Biobank, while the COIN cohort provided healthcare utilization data. RESULTS In the Dutch IBD Biobank study, 2118 CD patients and 1269 UC patients were analyzed. Female CD patients were more often current smokers, and male UC patients were more often previous smokers. Early onset CD (<16 years) was more frequently encountered in males than in females (20% versus 12%, P < 0.01). Male CD patients were more often diagnosed with ileal disease (28% versus 20%, P < 0.01) and underwent more often small bowel and ileocecal resection. Extraintestinal manifestations (EIMs) were more often encountered in female IBD patients. In the COIN study, 1139 CD patients and 1213 UC patients were analyzed. Male CD patients used prednisone more often and suffered more often from osteopenia. IBD-specific healthcare costs did not differ between male and female IBD patients. CONCLUSIONS Sex differences in patients with IBD include age of onset, disease location, and EIM prevalence. No large differences in therapeutic management of IBD were observed between men and women with IBD. 10.1093/ibd/izy004_video1izy004_Video_15786481854001.
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Affiliation(s)
- Mirjam Severs
- Department of Gastroenterology and Hepatology, University Medical Center, Utrecht, Utrecht, The Netherlands
| | - Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Marie-Josée J Mangen
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, Utrecht, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Frank Hoentjen
- Department of Gastroenterology and Hepatology, University Medical Center St. Radboud, Nijmegen, The Netherlands
| | | | - Marieke Pierik
- Department of Gastroenterology and Hepatology, University Medical Center Maastricht, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam Medical Center, Amsterdam, The Netherlands
| | - Gerd Bouma
- Department of Gastroenterology and Hepatology, VU University Medical Center, Amsterdam, The Netherlands
| | - Janneke C van der Woude
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mirthe E van der Valk
- Department of Gastroenterology and Hepatology, University Medical Center, Utrecht, Utrecht, The Netherlands
| | - Marielle J L Romberg-Camps
- Department of Gastroenterology and Hepatology (Co-MIK), Zuyderland Medical Center, Sittard-Geleen, The Netherlands
| | - Cees H M Clemens
- Department of Gastroenterology and Hepatology, Diaconessenhuis, Leiden, The Netherlands
| | - Paul van de Meeberg
- Department of Gastroenterology and Hepatology, Slingeland Hospital, Doetinchem, The Netherlands
| | - Nofel Mahmmod
- Department of Gastroenterology and Hepatology, Antonius Hospital, Nieuwegein, The Netherlands
| | - Jeroen Jansen
- Department of Gastroenterology and Hepatology, Onze Lieve Vrouwe Gasthuis, Amsterdam, The Netherlands
| | - Bindia Jharap
- Department of Gastroenterology and Hepatology, Meander Medical Center, Amersfoort, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Center, Utrecht, Utrecht, The Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University Medical Center, Utrecht, Utrecht, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Herma H Fidder
- Department of Gastroenterology and Hepatology, University Medical Center, Utrecht, Utrecht, The Netherlands
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7
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Visschedijk MC, Spekhorst LM, Cheng SC, van Loo ES, Jansen BHD, Blokzijl T, Kil H, de Jong DJ, Pierik M, Maljaars JPWJ, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Nieuwenhuijs VB, Imhann F, van Sommeren S, Alberts R, Xavier RJ, Dijkstra G, Nico Faber K, Aldaz CM, Weersma RK, Festen EAM. Genomic and Expression Analyses Identify a Disease-Modifying Variant for Fibrostenotic Crohn's Disease. J Crohns Colitis 2018; 12:582-588. [PMID: 29361163 DOI: 10.1093/ecco-jcc/jjy001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 01/16/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Crohn's disease [CD] is a chronic inflammatory disease with unpredictable behaviour. More than half of CD patients eventually develop complications such as stenosis, for which they then require endoscopic dilatation or surgery, as no anti-fibrotic drugs are currently available. We aim to identify disease-modifying genes associated with fibrostenotic CD. METHODS We performed a within-case analysis comparing 'extreme phenotypes' using the Immunochip and replication of the top single nucleotide polymorphisms [SNPs] with Agena Bioscience in two independent case-control cohorts totalling 322 cases with fibrostenotis [recurrent after surgery] and 619 cases with purely inflammatory CD. RESULTS Combined meta-analysis resulted in a genome-wide significant signal for SNP rs11861007 [p = 6.0910-11], located on chromosome 16, in lncRNA RP11-679B19.1, an lncRNA of unknown function, and close to exon 9 of the WWOX gene, which codes for WW domain-containing oxidoreductase. We analysed mRNA expression of TGF-β and downstream genes in ileocecal resection material from ten patients with and without the WWOX risk allele. Patients carrying the risk allele [A] showed enhanced colonic expression of TGF-β compared to patients homozygous for the wild-type [G] allele [p = 0.0079]. CONCLUSION We have identified a variant in WWOX and in lncRNA RP11-679B19.1 as a disease-modifying genetic variant associated with recurrent fibrostenotic CD and replicated this association in an independent cohort. WWOX can potentially play a crucial role in fibrostenosis in CD, being positioned at the crossroads of inflammation and fibrosis.
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Affiliation(s)
- Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Ellen S van Loo
- Department of Surgery, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - B H Dianne Jansen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Tjasso Blokzijl
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hyunsuk Kil
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas M.D. Anderson Cancer Centre, Smithville, USA
| | - Dirk J de Jong
- Department of Gastroenterology and Hepatology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Marieke Pierik
- Division of Gastroenterology and Hepatology, University Medical Centre Maastricht, Maastricht, The Netherlands
| | - Jeroen P W J Maljaars
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - C Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Adriaan A van Bodegraven
- Department of Gastroenterology and Hepatology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Academic Medical Centre, Amsterdam, The Netherlands
| | | | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Suzanne van Sommeren
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Rudi Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Laboratory Medicine, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - C Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas M.D. Anderson Cancer Centre, Smithville, USA
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, The Netherlands
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8
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Imhann F, Vila AV, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 2018; 67:108-119. [PMID: 27802154 PMCID: PMC5699972 DOI: 10.1136/gutjnl-2016-312135] [Citation(s) in RCA: 460] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/15/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Patients with IBD display substantial heterogeneity in clinical characteristics. We hypothesise that individual differences in the complex interaction of the host genome and the gut microbiota can explain the onset and the heterogeneous presentation of IBD. Therefore, we performed a case-control analysis of the gut microbiota, the host genome and the clinical phenotypes of IBD. DESIGN Stool samples, peripheral blood and extensive phenotype data were collected from 313 patients with IBD and 582 truly healthy controls, selected from a population cohort. The gut microbiota composition was assessed by tag-sequencing the 16S rRNA gene. All participants were genotyped. We composed genetic risk scores from 11 functional genetic variants proven to be associated with IBD in genes that are directly involved in the bacterial handling in the gut: NOD2, CARD9, ATG16L1, IRGM and FUT2. RESULTS Strikingly, we observed significant alterations of the gut microbiota of healthy individuals with a high genetic risk for IBD: the IBD genetic risk score was significantly associated with a decrease in the genus Roseburia in healthy controls (false discovery rate 0.017). Moreover, disease location was a major determinant of the gut microbiota: the gut microbiota of patients with colonic Crohn's disease (CD) is different from that of patients with ileal CD, with a decrease in alpha diversity associated to ileal disease (p=3.28×10-13). CONCLUSIONS We show for the first time that genetic risk variants associated with IBD influence the gut microbiota in healthy individuals. Roseburia spp are acetate-to-butyrate converters, and a decrease has already been observed in patients with IBD.
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Affiliation(s)
- Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Dirk Gevers
- Broad Institute of Harvard and MIT, Boston, USA
| | - Marijn C. Visschedijk
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lieke M. Spekhorst
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rudi Alberts
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Hendrik M. van Dullemen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Rinze W.F. Ter Steege
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Curtis Huttenhower
- Broad Institute of Harvard and MIT, Boston, USA,Biostatistics Department, Harvard School of Public Health, Boston, USA
| | - Gerard Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Ramnik J. Xavier
- Broad Institute of Harvard and MIT, Boston, USA,Massachusetts General Hospital, Boston, USA
| | - Eleonora A.M. Festen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rinse K. Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
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9
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Spekhorst LM, Oldenburg B, van Bodegraven AA, de Jong DJ, Imhann F, van der Meulen-de Jong AE, Pierik MJ, van der Woude JC, Dijkstra G, D’Haens G, Löwenberg M, Weersma RK, Festen EAM. Prevalence of- and risk factors for work disability in Dutch patients with inflammatory bowel disease. World J Gastroenterol 2017; 23:8182-8192. [PMID: 29290654 PMCID: PMC5739924 DOI: 10.3748/wjg.v23.i46.8182] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/26/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To determine the prevalence of work disability in inflammatory bowel disease (IBD), and to assess risk factors associated with work disability.
METHODS For this retrospective cohort study, we retrieved clinical data from the Dutch IBD Biobank on July 2014, containing electronic patient records of 3388 IBD patients treated in the eight University Medical Centers in the Netherlands. Prevalence of work disability was assessed in 2794 IBD patients and compared with the general Dutch population. Multivariate analyses were performed for work disability (sick leave, partial and full disability) and long-term full work disability (> 80% work disability for > 2 years).
RESULTS Prevalence of work disability was higher in Crohn’s disease (CD) (29%) and ulcerative colitis (UC) (19%) patients compared to the general Dutch population (7%). In all IBD patients, female sex, a lower education level, and extra-intestinal manifestations, were associated with work disability. In CD patients, an age > 40 years at diagnosis, disease duration > 15 years, smoking, surgical interventions, and anti-TNFα use were associated with work disability. In UC patients, an age > 55 years, and immunomodulator use were associated with work disability. In CD patients, a lower education level (OR = 1.62, 95%CI: 1.02-2.58), and in UC patients, disease complications (OR = 3.39, 95%CI: 1.09-10.58) were associated with long-term full work disability.
CONCLUSION The prevalence of work disability in IBD patients is higher than in the general Dutch population. Early assessment of risk factors for work disability is necessary, as work disability is substantial among IBD patients.
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Affiliation(s)
- Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Center Utrecht, Utrecht, 3584 CX Utrecht, the Netherlands
| | - Ad A van Bodegraven
- Department of Gastroenterology and Hepatology, VU University Medical Center, Amsterdam, 1081 HV Amsterdam, the Netherlands
| | - Dirk J de Jong
- Department of Gastroenterology and Hepatology, University Medical Center St. Radboud, Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
| | | | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, University Medical Center Maastricht, Maastricht, 6229 HX Maastricht, the Netherlands
| | - Janneke C van der Woude
- Department of Gastroenterology and Hepatology, Erasmus Medical Center, the Netherlands, Rotterdam, 3015 CE Rotterdam, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
| | - Geert D’Haens
- Department of Gastroenterology and Hepatology, Amsterdam Medical Center, Amsterdam, 1105 AZ Amsterdam-Zuidoost, the Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam Medical Center, Amsterdam, 1105 AZ Amsterdam-Zuidoost, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Centre Groningen, Groningen, 9700 RB Groningen, the Netherlands
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10
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Spekhorst LM, Severs M, de Boer NKH, Festen EAM, Fidder HH, Hoentjen F, Imhann F, de Jong DJ, van der Meulen-de Jong AE, Pierik MJ, van der Woude CJ, Dijkstra G, Ponsioen CY, Löwenberg M, Oldenburg B, Weersma RK. The Impact of Ethnicity and Country of Birth on Inflammatory Bowel Disease Phenotype: a Prospective Cohort Study. J Crohns Colitis 2017; 11:1463-1470. [PMID: 28981621 DOI: 10.1093/ecco-jcc/jjx098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/20/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS The number of patients with inflammatory bowel disease [IBD], of non-Caucasian descent in Western Europe, is increasing. We aimed to explore the impact of ethnicity and country of birth on IBD phenotype. METHODS IBD patients treated in the eight University Medical Centers in The Netherlands [Dutch IBD Biobank] were divided into two groups according to their ethnicity: 1] Caucasian patients of Western and Central European descent [CEU]; and 2] patients of non-Caucasian descent [non-CEU]. The non-CEU group was subdivided according to country of birth, into: born in The Netherlands or Western Europe [non-CEU European born]; or born outside Western-Europe who migrated to The Netherlands [non-CEU non-European born]. Both comparisons were analysed for phenotype differences [by chi-square test]. RESULTS The Dutch IBD Biobank included 2921 CEU patients and 233 non-CEU patients. Non-CEU Crohn's disease [CD] patients more often had upper gastro-intestinal disease [16% vs 8%, p = 0.001] and anal stenosis [10% vs 4%, p = 0.002] than CEU CD patients. The use of anti-tumour necrosis factor [TNF] agents and immunomodulators was higher in non-CEU IBD patients than in CEU IBD patients [45% vs 38%, p = 0.042] and [77% vs 66%, p = 0.001], respectively. Non-CEU IBD patients born in Europe [n = 116] were diagnosed at a lower age than non-CEU IBD patients born outside Europe [n = 115] [at 22.7 vs 28.9 years old, p < 0.001]. CONCLUSION Non-Caucasians had more severe disease behaviour than Caucasians. Non-CEU patients born in Europe were diagnosed at a lower age with IBD than those born outside Europe who migrated to The Netherlands.
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Affiliation(s)
- L M Spekhorst
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, The Netherlands
| | - M Severs
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, The Netherlands
| | - N K H de Boer
- Department of Gastroenterology and Hepatology, VU University Medical Centre, The Netherlands
| | - E A M Festen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, The Netherlands
| | - H H Fidder
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, The Netherlands
| | - F Hoentjen
- Department of Gastroenterology and Hepatology, University Medical Centre St. Radboud, The Netherlands
| | - F Imhann
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, The Netherlands
| | - D J de Jong
- Department of Gastroenterology and Hepatology, University Medical Centre St. Radboud, The Netherlands
| | | | - M J Pierik
- Department of Gastroenterology and Hepatology, University Medical Centre Maastricht, The Netherlands
| | - C J van der Woude
- Department of Gastroenterology and Hepatology, Erasmus Medical Centre, The Netherlands
| | - G Dijkstra
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, The Netherlands
| | - C Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam Medical Centre, The Netherlands
| | - M Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam Medical Centre, The Netherlands
| | - B Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, The Netherlands
| | - R K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, The Netherlands
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11
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Spekhorst LM, Imhann F, Festen EAM, van Bodegraven AA, de Boer NKH, Bouma G, Fidder HH, d'Haens G, Hoentjen F, Hommes DW, de Jong DJ, Löwenberg M, Maljaars PWJ, van der Meulen-de Jong AE, Oldenburg B, Pierik MJ, Ponsioen CY, Stokkers PC, Verspaget HW, Visschedijk MC, van der Woude CJ, Dijkstra G, Weersma RK. Cohort profile: design and first results of the Dutch IBD Biobank: a prospective, nationwide biobank of patients with inflammatory bowel disease. BMJ Open 2017; 7:e016695. [PMID: 29122790 PMCID: PMC5695377 DOI: 10.1136/bmjopen-2017-016695] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE The Dutch IBD Biobank aims to facilitate the discovery of predictors for individual disease course and treatment response in patients with inflammatory bowel disease (IBD). In this paper, we aim to describe the establishment of the Dutch IBD Biobank, including the facilitators and barriers to establishment. Moreover, we aim to provide a complete overview of the content of the Dutch IBD Biobank. PARTICIPANTS Since 2007, every patient with IBD treated in one of the eight Dutch university medical centres is asked to participate in the Dutch IBD Biobank in which 225 standardised IBD-related data items and biomaterials, such as serum, DNA, biopsies and a stool sample, are collected. FINDINGS TO DATE As of June 2014, the Dutch IBD Biobank had enrolled 3388 patients with IBD: 2118 Crohn's disease (62.5%), 1190 ulcerative colitis (35.1%), 74 IBD-unclassified (2.2%) and 6 IBD-indeterminate (0.2%). The inclusion of patients with IBD is ongoing. The quality of the biomaterials is good and serum, DNA and biopsies have been used in newly published studies. FUTURE PLANS The genotyping (750 000 genetic variants) of all participants of the Dutch IBD Biobank is currently ongoing, enabling more genetic research. In addition, all participants will start reporting disease activity and outcome measures using an online platform and mobile app.
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Affiliation(s)
- Lieke M Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen and Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Ad A van Bodegraven
- Department of Gastroenterology and Hepatology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Nanne K H de Boer
- Department of Gastroenterology and Hepatology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Gerd Bouma
- Department of Gastroenterology and Hepatology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Herma H Fidder
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Geert d'Haens
- Department of Gastroenterology and Hepatology, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - Frank Hoentjen
- Department of Gastroenterology and Hepatology, University Medical Centre St. Radboud, Nijmegen, The Netherlands
| | - Daan W Hommes
- UCLA Center for Inflammatory Bowel Diseases, Division of Digestive Diseases, David Geffen School of Medicine, University of California, California, Los Angeles, USA
| | - Dirk J de Jong
- Department of Gastroenterology and Hepatology, University Medical Centre St. Radboud, Nijmegen, The Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - P W Jeroen Maljaars
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marieke J Pierik
- Department of Gastroenterology and Hepatology, University Medical Centre Maastricht, Maastricht, The Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - Pieter C Stokkers
- Department of Gastroenterology and Hepatology, St Lucas Andreas Ziekenhuis, Amsterdam, The Netherlands
| | - Hein W Verspaget
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and Medical Center Groningen, Groningen, The Netherlands
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12
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Visschedijk MC, Alberts R, Mucha S, Deelen P, de Jong DJ, Pierik M, Spekhorst LM, Imhann F, van der Meulen-de Jong AE, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Dijkstra G, Ellinghaus D, Schreiber S, Wijmenga C, Rivas MA, Franke A, van Diemen CC, Weersma RK. Pooled Resequencing of 122 Ulcerative Colitis Genes in a Large Dutch Cohort Suggests Population-Specific Associations of Rare Variants in MUC2. PLoS One 2016; 11:e0159609. [PMID: 27490946 PMCID: PMC4973970 DOI: 10.1371/journal.pone.0159609] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/05/2016] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies have revealed several common genetic risk variants for ulcerative colitis (UC). However, little is known about the contribution of rare, large effect genetic variants to UC susceptibility. In this study, we performed a deep targeted re-sequencing of 122 genes in Dutch UC patients in order to investigate the contribution of rare variants to the genetic susceptibility to UC. The selection of genes consists of 111 established human UC susceptibility genes and 11 genes that lead to spontaneous colitis when knocked-out in mice. In addition, we sequenced the promoter regions of 45 genes where known variants exert cis-eQTL-effects. Targeted pooled re-sequencing was performed on DNA of 790 Dutch UC cases. The Genome of the Netherlands project provided sequence data of 500 healthy controls. After quality control and prioritization based on allele frequency and pathogenicity probability, follow-up genotyping of 171 rare variants was performed on 1021 Dutch UC cases and 1166 Dutch controls. Single-variant association and gene-based analyses identified an association of rare variants in the MUC2 gene with UC. The associated variants in the Dutch population could not be replicated in a German replication cohort (1026 UC cases, 3532 controls). In conclusion, this study has identified a putative role for MUC2 on UC susceptibility in the Dutch population and suggests a population-specific contribution of rare variants to UC.
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Affiliation(s)
- Marijn C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, 9700 RB, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9700 RB, Groningen, The Netherlands
| | - Rudi Alberts
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, 9700 RB, Groningen, The Netherlands
| | - Soren Mucha
- Institute of Clinical Molecular Biology, Kiel University, D-24105, Kiel, Germany
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9700 RB, Groningen, The Netherlands
| | - Dirk J. de Jong
- Department of Gastroenterology and Hepatology, Radboud University Nijmegen Medical Centre, 6525 GA, Nijmegen, The Netherlands
| | - Marieke Pierik
- Division of Gastroenterology and Hepatology, Maastricht University Medical Centre, 6229 HX, Maastricht, The Netherlands
| | - Lieke M. Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, 9700 RB, Groningen, The Netherlands
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, 9700 RB, Groningen, The Netherlands
| | | | - C. Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus University Medical Centre, 3015 CE, Rotterdam, The Netherlands
| | - Adriaan A. van Bodegraven
- Department of Gastroenterology and Hepatology, VU University Medical Centre, 1081 HZ, Amsterdam, The Netherlands
| | - Bas Oldenburg
- Department of Gastroenterology and Hepatology, University Medical Centre Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Mark Löwenberg
- Department of Gastroenterology and Hepatology, Academic Medical Centre, 1105 AZ, Amsterdam, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, 9700 RB, Groningen, The Netherlands
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, D-24105, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Centre Schleswig-Holstein, Kiel, Germany
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9700 RB, Groningen, The Netherlands
| | | | | | - Manuel A. Rivas
- Centre for the Study of IBD (SCIBD) Genetics, The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, D-24105, Kiel, Germany
| | - Cleo C. van Diemen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, 9700 RB, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, 9700 RB, Groningen, The Netherlands
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Spekhorst LM, Visschedijk MC, Weersma RK, Festen EA. Down the line from genome-wide association studies in inflammatory bowel disease: the resulting clinical benefits and the outlook for the future. Expert Rev Clin Immunol 2014; 11:33-44. [DOI: 10.1586/1744666x.2015.990439] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Spekhorst LM, Visschedijk MC, Alberts R, Festen EA, van der Wouden EJ, Dijkstra G, (ICC) RKWDIOCAC. Performance of the Montreal classification for inflammatory bowel diseases. World J Gastroenterol 2014; 20:15374-15381. [PMID: 25386087 PMCID: PMC4223272 DOI: 10.3748/wjg.v20.i41.15374] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/30/2014] [Accepted: 07/25/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To validate the Montreal classification system for Crohn’s disease (CD) and ulcerative colitis (UC) within the Netherlands.
METHODS: A selection of 20 de-identified medical records with an appropriate representation of the inflammatory bowel disease (IBD) sub phenotypes were scored by 30 observers with different professions (gastroenterologist specialist in IBD, gastroenterologist in training and IBD-nurses) and experience level with IBD patient care. Patients were classified according to the Montreal classification. In addition, participants were asked to score extra-intestinal manifestations (EIM) and disease severity in CD based on their clinical judgment. The inter-observer agreement was calculated by percentages of correct answers (answers identical to the “expert evaluation”) and Fleiss-kappa (κ). Kappa cut-offs: < 0.4-poor; 0.41-0.6-moderate; 0.61-0.8-good; > 0.8 excellent.
RESULTS: The inter-observer agreement was excellent for diagnosis (κ = 0.96), perianal disease (κ = 0.92) and disease location in CD (κ = 0.82) and good for age of onset (κ = 0.67), upper gastrointestinal disease (κ = 0.62), disease behaviour in CD (κ = 0.79) and disease extent in UC (κ = 0.65). Disease severity in UC was scored poor (κ = 0.23). The additional items resulted in a good inter-observer agreement for EIM (κ = 0.68) and a moderate agreement for disease severity in CD (κ = 0.44). Percentages of correct answers over all Montreal items give a good reflection of the inter-observer agreement (> 80%), except for disease severity (48%-74%). IBD-nurses were significantly worse in scoring upper gastrointestinal disease in CD compared to gastroenterologists (P = 0.008) and gastroenterologists in training (P = 0.040). Observers with less than 10 years of experience were significantly better at scoring UC severity than observers with 10-20 years (P = 0.003) and more than 20 years (P = 0.003) of experience with IBD patient care. Observers with 10-20 years of experience with IBD patient care were significantly better at scoring upper gastrointestinal disease in CD than observers with less than 10 years (P = 0.007) and more than 20 years (P = 0.007) of experience with IBD patient care.
CONCLUSION: We found a good to excellent inter-observer agreement for all Montreal items except for disease severity in UC (poor).
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