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Brushett S, Gacesa R, Vich Vila A, Brandao Gois M, Andreu-Sánchez S, Swarte J, Klaassen M, Collij V, Sinha T, Bolte L, Wu J, Swertz M, de Kroon M, Reijneveld S, Wijmenga C, Weersma R, Fu J, van Loo H, Kurilshikov A, Zhernakova A. Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome. Gut Microbes 2023; 15:2281360. [PMID: 38017662 PMCID: PMC10730195 DOI: 10.1080/19490976.2023.2281360] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
The gut microbiome is involved in the bi-directional relationship of the gut - brain axis. As most studies of this relationship are small and do not account for use of psychotropic drugs (PTDs), we explored the relations of the gut microbiome with several internalizing disorders, while adjusting for PTDs and other relevant medications, in 7,656 Lifelines participants from the Northern Netherlands (5,522 controls and 491 participants with at least one internalizing disorder). Disorders included dysthymia, major depressive disorder (MDD), any depressive disorder (AnyDep: dysthymia or MDD), generalized anxiety disorder (GAD) and any anxiety disorder (AnyAnx: GAD, social phobia and panic disorder). Compared to controls, 17 species were associated with depressive disorders and 3 were associated with anxiety disorders. Around 90% of these associations remained significant (FDR <0.05) after adjustment for PTD use, suggesting that the disorders, not PTD use, drove these associations. Negative associations were observed for the butyrate-producing bacteria Ruminococcus bromii in participants with AnyDep and for Bifidobacterium bifidum in AnyAnx participants, along with many others. Tryptophan and glutamate synthesis modules and the 3,4-Dihydroxyphenylacetic acid synthesis module (related to dopamine metabolism) were negatively associated with MDD and/or dysthymia. After additional adjustment for functional gastrointestinal disorders and irritable bowel syndrome, these relations remained either statistically (FDR <0.05) or nominally (P < 0.05) significant. Overall, multiple bacterial species and functional modules were associated with internalizing disorders, including gut - brain relevant components, while associations to PTD use were moderate. These findings suggest that internalizing disorders rather than PTDs are associated with gut microbiome differences relative to controls.
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Affiliation(s)
- S. Brushett
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Health Sciences, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R. Gacesa
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - A. Vich Vila
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - M.F. Brandao Gois
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - S. Andreu-Sánchez
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J.C. Swarte
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - M.A.Y. Klaassen
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - V. Collij
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - T. Sinha
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - L.A. Bolte
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J. Wu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - M. Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - M.L.A. de Kroon
- Department of Health Sciences, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - S.A. Reijneveld
- Department of Health Sciences, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C. Wijmenga
- 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
| | - J. Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - H.M. van Loo
- Department of Psychiatry, Interdisciplinary Center Psychopathology and Emotion regulation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - A. Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - A. Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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2
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Vangeenderhuysen P, Van Arnhem J, Pomian B, De Graeve M, De Commer L, Falony G, Raes J, Zhernakova A, Fu J, Hemeryck LY, Vanhaecke L. Dual UHPLC-HRMS Metabolomics and Lipidomics and Automated Data Processing Workflow for Comprehensive High-Throughput Gut Phenotyping. Anal Chem 2023. [PMID: 37220321 DOI: 10.1021/acs.analchem.2c05371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In recent years, feces has surfaced as the matrix of choice for investigating the gut microbiome-health axis because of its non-invasive sampling and the unique reflection it offers of an individual's lifestyle. In cohort studies where the number of samples required is large, but availability is scarce, a clear need exists for high-throughput analyses. Such analyses should combine a wide physicochemical range of molecules with a minimal amount of sample and resources and downstream data processing workflows that are as automated and time efficient as possible. We present a dual fecal extraction and ultra high performance liquid chromatography-high resolution-quadrupole-orbitrap-mass spectrometry (UHPLC-HR-Q-Orbitrap-MS)-based workflow that enables widely targeted and untargeted metabolome and lipidome analysis. A total of 836 in-house standards were analyzed, of which 360 metabolites and 132 lipids were consequently detected in feces. Their targeted profiling was validated successfully with respect to repeatability (78% CV < 20%), reproducibility (82% CV < 20%), and linearity (81% R2 > 0.9), while also enabling holistic untargeted fingerprinting (15,319 features, CV < 30%). To automate targeted processing, we optimized an R-based targeted peak extraction (TaPEx) algorithm relying on a database comprising retention time and mass-to-charge ratio (360 metabolites and 132 lipids), with batch-specific quality control curation. The latter was benchmarked toward vendor-specific targeted and untargeted software and our isotopologue parameter optimization/XCMS-based untargeted pipeline in LifeLines Deep cohort samples (n = 97). TaPEx clearly outperformed the untargeted approaches (81.3 vs 56.7-66.0% compounds detected). Finally, our novel dual fecal metabolomics-lipidomics-TaPEx method was successfully applied to Flemish Gut Flora Project cohort (n = 292) samples, leading to a sample-to-result time reduction of 60%.
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Affiliation(s)
- P Vangeenderhuysen
- Laboratory of Integrative Metabolomics (LIMET), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - J Van Arnhem
- Laboratory of Integrative Metabolomics (LIMET), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - B Pomian
- Laboratory of Integrative Metabolomics (LIMET), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - M De Graeve
- Laboratory of Integrative Metabolomics (LIMET), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - L De Commer
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- VIB, Center for Microbiology, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - G Falony
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- VIB, Center for Microbiology, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - J Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
- VIB, Center for Microbiology, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - A Zhernakova
- Department of Genetics, University of Groningen, Antonius Deusinglaan 1, 9700 AB Groningen, The Netherlands
| | - J Fu
- Department of Genetics, University of Groningen, Antonius Deusinglaan 1, 9700 AB Groningen, The Netherlands
- Department of Pediatrics, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - L Y Hemeryck
- Laboratory of Integrative Metabolomics (LIMET), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - L Vanhaecke
- Laboratory of Integrative Metabolomics (LIMET), Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
- Institute for Global Food Security, School of Biological Sciences, Queen's University, University Road, BT7 1NN Belfast, Northern Ireland, U.K
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3
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Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, Andreu-Sánchez S, Chen L, Collij V, Hu S, Dekens JAM, Lenters VC, Björk JR, Swarte JC, Swertz MA, Jansen BH, Gelderloos-Arends J, Jankipersadsing S, Hofker M, Vermeulen RCH, Sanna S, Harmsen HJM, Wijmenga C, Fu J, Zhernakova A, Weersma RK. Environmental factors shaping the gut microbiome in a Dutch population. Nature 2022; 604:732-739. [PMID: 35418674 DOI: 10.1038/s41586-022-04567-7] [Citation(s) in RCA: 198] [Impact Index Per Article: 99.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/18/2022] [Indexed: 12/22/2022]
Abstract
The gut microbiome is associated with diverse diseases1-3, but a universal signature of a healthy or unhealthy microbiome has not been identified, and there is a need to understand how genetics, exposome, lifestyle and diet shape the microbiome in health and disease. Here we profiled bacterial composition, function, antibiotic resistance and virulence factors in the gut microbiomes of 8,208 Dutch individuals from a three-generational cohort comprising 2,756 families. We correlated these to 241 host and environmental factors, including physical and mental health, use of medication, diet, socioeconomic factors and childhood and current exposome. We identify that the microbiome is shaped primarily by the environment and cohabitation. Only around 6.6% of taxa are heritable, whereas the variance of around 48.6% of taxa is significantly explained by cohabitation. By identifying 2,856 associations between the microbiome and health, we find that seemingly unrelated diseases share a common microbiome signature that is independent of comorbidities. Furthermore, we identify 7,519 associations between microbiome features and diet, socioeconomics and early life and current exposome, with numerous early-life and current factors being significantly associated with microbiome function and composition. Overall, this study provides a comprehensive overview of gut microbiome and the underlying impact of heritability and exposures that will facilitate future development of microbiome-targeted therapies.
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Affiliation(s)
- R Gacesa
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A Vich Vila
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - T Sinha
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M A Y Klaassen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - L A Bolte
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Andreu-Sánchez
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - L Chen
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - V Collij
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Hu
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J A M Dekens
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Center of Development and Innovation, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - V C Lenters
- University Medical Centre Utrecht, Julius Center for Health Sciences and Primary Care, Utrecht, The Netherlands
| | - J R Björk
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J C Swarte
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M A Swertz
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - B H Jansen
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J Gelderloos-Arends
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - S Jankipersadsing
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M Hofker
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - R C H Vermeulen
- University Medical Centre Utrecht, Julius Center for Health Sciences and Primary Care, Utrecht, The Netherlands.,Utrecht University, Institute for Risk Assessment Sciences (IRAS), Department of Population Health Sciences, Utrecht, The Netherlands
| | - S Sanna
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.,Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Cagliari, Italy
| | - H J M Harmsen
- Department of Medical Microbiology and Infection prevention, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - C Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - J Fu
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands. .,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.
| | - A Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - R K Weersma
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands.
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4
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Gacesa R, Vich Vila A, Collij V, Mujagic Z, Kurilshikov A, Voskuil M, Festen E, Wijmenga C, Jonkers D, Dijkstra G, Fu J, Zhernakova A, Imhann F, Weersma R. A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease. Gut Microbes 2021; 13:1943288. [PMID: 34313538 PMCID: PMC8317932 DOI: 10.1080/19490976.2021.1943288] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) show a large overlap in clinical presentation, which presents diagnostic challenges. As a consequence, invasive and burdensome endoscopies are often used to distinguish between IBD and IBS. Here, we aimed to develop a noninvasive fecal test that can distinguish between IBD and IBS and reduce the number of endoscopies.We used shotgun metagenomic sequencing to analyze the composition and function of gut microbiota of 169 IBS patients, 447 IBD patients and 1044 population controls and measured fecal Calprotectin (FCal), human beta defensin 2 (HBD2), and chromogranin A (CgA) in these samples. These measurements were used to construct training sets (75% of data) for logistic regression and machine learning models to differentiate IBS from IBD and inactive from active IBD. The results were replicated on test sets (remaining 25% of the data) and microbiome data obtained using 16S sequencing.Fecal HBD2 showed high sensitivity and specificity for differentiating between IBD and IBS (sensitivity = 0.89, specificity = 0.76), while the inclusion of microbiome data with biomarkers (HBD2 and FCal) showed a potential for improvement in predictive power (optimal sensitivity = 0.87, specificity = 0.93). Shotgun sequencing-based models produced comparable results using 16S-sequencing data. HBD2 and FCal were found to have predictive power for IBD disease activity (AUC ≈ 0.7).HBD2 is a novel biomarker for IBD in patients with gastro-intestinal complaints, especially when used in combination with FCal and potentially in combination with gut microbiome data.
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Affiliation(s)
- R. Gacesa
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - A. Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - V. Collij
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Z. Mujagic
- Maastricht University Medical Center, Division of Gastroenterology-Hepatology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, The Netherlands
| | - A. Kurilshikov
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M.D. Voskuil
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - E.A.M. Festen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - C. Wijmenga
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - D.M.A.E. Jonkers
- Maastricht University Medical Center, Division of Gastroenterology-Hepatology, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht, The Netherlands
| | - G. Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - J. Fu
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - A. Zhernakova
- University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - F. Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands,University of Groningen and University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands,CONTACT F. Imhann University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - R.K. Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
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5
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van den Munckhof ICL, Kurilshikov A, Ter Horst R, Riksen NP, Joosten LAB, Zhernakova A, Fu J, Keating ST, Netea MG, de Graaf J, Rutten JHW. Role of gut microbiota in chronic low-grade inflammation as potential driver for atherosclerotic cardiovascular disease: a systematic review of human studies. Obes Rev 2018; 19:1719-1734. [PMID: 30144260 DOI: 10.1111/obr.12750] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [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: 01/29/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
A hallmark of obesity is chronic low-grade inflammation, which plays a major role in the process of atherosclerotic cardiovascular disease (ACVD). Gut microbiota is one of the factors influencing systemic immune responses, and profound changes have been found in its composition and metabolic function in individuals with obesity. This systematic review assesses the association between the gut microbiota and markers of low-grade inflammation in humans. We identified 14 studies which were mostly observational and relatively small (n = 10 to 471). The way in which the microbiome is analysed differed extensively between these studies. Lower gut microbial diversity was associated with higher white blood cell counts and high sensitivity C-reactive protein (hsCRP) levels. The abundance of Bifidobacterium, Faecalibacterium, Ruminococcus and Prevotella were inversely related to different markers of low-grade inflammation such as hsCRP and interleukin (IL)-6. In addition, this review speculates on possible mechanisms through which the gut microbiota can affect low-grade inflammation and thereby ACVD. We discuss the associations between the microbiome and the inflammasome, the innate immune system, bile acids, gut permeability, the endocannabinoid system and TMAO. These data reinforce the importance of human research into the gut microbiota as potential diagnostic and therapeutic strategy to prevent ACVD.
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Affiliation(s)
- I C L van den Munckhof
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - A Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - R Ter Horst
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N P Riksen
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - L A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - A Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - J Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - S T Keating
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M G Netea
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department for Genomics and Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - J de Graaf
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J H W Rutten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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6
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Bonfiglio F, Henström M, Nag A, Hadizadeh F, Zheng T, Cenit MC, Tigchelaar E, Williams F, Reznichenko A, Ek WE, Rivera NV, Homuth G, Aghdassi AA, Kacprowski T, Männikkö M, Karhunen V, Bujanda L, Rafter J, Wijmenga C, Ronkainen J, Hysi P, Zhernakova A, D'Amato M. A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome. Neurogastroenterol Motil 2018; 30:e13358. [PMID: 29673008 DOI: 10.1111/nmo.13358] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 11/20/2017] [Accepted: 03/23/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Irritable bowel syndrome (IBS) shows genetic predisposition, however, large-scale, powered gene mapping studies are lacking. We sought to exploit existing genetic (genotype) and epidemiological (questionnaire) data from a series of population-based cohorts for IBS genome-wide association studies (GWAS) and their meta-analysis. METHODS Based on questionnaire data compatible with Rome III Criteria, we identified a total of 1335 IBS cases and 9768 asymptomatic individuals from 5 independent European genotyped cohorts. Individual GWAS were carried out with sex-adjusted logistic regression under an additive model, followed by meta-analysis using the inverse variance method. Functional annotation of significant results was obtained via a computational pipeline exploiting ontology and interaction networks, and tissue-specific and gene set enrichment analyses. KEY RESULTS Suggestive GWAS signals (P ≤ 5.0 × 10-6 ) were detected for 7 genomic regions, harboring 64 gene candidates to affect IBS risk via functional or expression changes. Functional annotation of this gene set convincingly (best FDR-corrected P = 3.1 × 10-10 ) highlighted regulation of ion channel activity as the most plausible pathway affecting IBS risk. CONCLUSION & INFERENCES Our results confirm the feasibility of population-based studies for gene-discovery efforts in IBS, identify risk genes and loci to be prioritized in independent follow-ups, and pinpoint ion channels as important players and potential therapeutic targets warranting further investigation.
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Affiliation(s)
- F Bonfiglio
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, Spain.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - M Henström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - A Nag
- Department of Twin Research & Genetic Epidemiology, King's College London, London, England
| | - F Hadizadeh
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - T Zheng
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - M C Cenit
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - E Tigchelaar
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - F Williams
- Department of Twin Research & Genetic Epidemiology, King's College London, London, England
| | - A Reznichenko
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - W E Ek
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory Uppsala, Uppsala University, Uppsala, Sweden
| | - N V Rivera
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - G Homuth
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - A A Aghdassi
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - T Kacprowski
- Department of Functional Genomics, Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - M Männikkö
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
| | - V Karhunen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Oulu University Hospital, Oulu, Finland.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - L Bujanda
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - J Rafter
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - C Wijmenga
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - J Ronkainen
- Center for Life Course Health Research, University of Oulu, Oulu, Finland.,Primary Health Care Center, Tornio, Finland
| | - P Hysi
- Department of Ophthalmology, King's College London, St Thomas' Hospital Campus, London, UK
| | - A Zhernakova
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - M D'Amato
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, Spain.,Unit of Clinical Epidemiology, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,BioCruces Health Research Institute, Bilbao, Spain.,IKERBASQUE, Basque Science Foundation, Bilbao, Spain
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7
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Tigchelaar EF, Mujagic Z, Zhernakova A, Hesselink MAM, Meijboom S, Perenboom CWM, Masclee AAM, Wijmenga C, Feskens EJM, Jonkers DMAE. Habitual diet and diet quality in Irritable Bowel Syndrome: A case-control study. Neurogastroenterol Motil 2017; 29. [PMID: 28714091 DOI: 10.1111/nmo.13151] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 12/20/2016] [Accepted: 06/09/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND Diet is considered to be a key factor in symptom generation in Irritable Bowel Syndrome (IBS) and patients tend to exclude food products from their diet in pursue of symptom relief, which may impair diet quality. METHODS We evaluated habitual dietary intake in IBS patients with regard to nutrients and food products using an extensive food frequency questionnaire. One hundred ninety-four IBS patients were compared to 186 healthy controls using multiple logistic regression analysis. An overall diet quality score was calculated for each participant based on the criteria of the Dutch Healthy Diet (DHD) index. KEY RESULTS A lower DHD-score was found for IBS (mean [SD]: 52.9 [9.6]) vs controls (55.1 [9.2], P=.02). The diet of patients was lower in fibers (21 g vs 25 g per day, P=.002) and fructose (14 g vs 16 g, P=.033), while higher in total fat (37% vs 36% of total energy intake, P=.010) and added sugars (46 g vs 44 g, P=.029). Differences in daily intake of food products included lower consumption of apples (40 g vs 69 g, P<.001), pasta (28 vs 37 g, P=.029) and alcoholic beverages (130 g vs 193 g, P=.024) and higher consumption of processed meat (38 g vs 29 g, P<.001). Some of these findings correlated with gastrointestinal symptoms, showing differences between IBS subtypes. CONCLUSIONS AND INFERENCES Differences in habitual diet were described, showing lower diet quality in IBS patients compared to controls, with increased consumption of fat and lower intake of fibers and fructose. Our data support the importance of personalized and professional nutritional guidance of IBS patients.
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Affiliation(s)
- E F Tigchelaar
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - Z Mujagic
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands.,Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - A Zhernakova
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - M A M Hesselink
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - S Meijboom
- Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - C W M Perenboom
- Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - A A M Masclee
- Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - C Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands
| | - E J M Feskens
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands.,Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - D M A E Jonkers
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands.,Division Gastroenterology-Hepatology, Department of Internal Medicine, NUTRIM School for Nutrition, and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
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8
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Blanchet L, Smolinska A, Baranska A, Tigchelaar E, Swertz M, Zhernakova A, Dallinga JW, Wijmenga C, van Schooten FJ. Factors that influence the volatile organic compound content in human breath. J Breath Res 2017; 11:016013. [PMID: 28140379 DOI: 10.1088/1752-7163/aa5cc5] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Thousands of endogenous and exogenous volatile organic compounds (VOCs) are excreted in each breath. Inflammatory and deviant metabolic processes affect the level of endogeneous VOCs, which can serve as specific biomarkers for clinical diagnosis and disease monitoring. Important issues that still need to be tackled are related to potential confounding factors like gender and age and endogenous and exogenous factors, like f.i. smoking. METHODS The aim of this study was to systematically access the effect of endogenous and exogenous factors on VOC composition of exhaled breath. In the current study breath samples from 1417 adult participants from the LifeLines cohort, a general population cohort in the Netherlands, were collected and the total content of VOCs was measured using gas chromatography-time-of-flight-mass spectrometry. Breath samples were collected in Groningen and transferred to carbon tubes immediately. These samples were then shipped to Maastricht and measured in batches. VOCs profiles were correlated to 14 relevant characteristics of all participants including age, BMI, smoking and blood cell counts and metabolic parameters as well as to 16 classes of medications. RESULTS VOCs profiles were shown to be significantly influenced by smoking behavior and to a lesser extent by age, BMI and gender. These factors need to be controlled for in breath analysis studies. We found no evidence whatsoever in this 1417 subjects' cohort that white blood cell counts, cholesterol or triglycerides levels have an influence on the VOC profile. Thus they may not have to be controlled for in exhaled breath studies. CONCLUSION The large cohort of volunteers used here represents a unique opportunity to gauge the factors influencing VOCs profiles in a general population i.e. the most clinically relevant population. Classical clinical parameters and smoking habits clearly influence breath content and should therefore be accounted for in future clinical studies involving breath analysis.
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Affiliation(s)
- L Blanchet
- Top Institute Food and Nutrition (TIFN), Wageningen, The Netherlands. Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre, Maastricht, The Netherlands. Thayer school of engineering, Dartmouth College, Hanover, NH, United States of America
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9
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Baranska A, Mujagic Z, Smolinska A, Dallinga JW, Jonkers DMAE, Tigchelaar EF, Dekens J, Zhernakova A, Ludwig T, Masclee AAM, Wijmenga C, van Schooten FJ. Volatile organic compounds in breath as markers for irritable bowel syndrome: a metabolomic approach. Aliment Pharmacol Ther 2016; 44:45-56. [PMID: 27136066 DOI: 10.1111/apt.13654] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [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: 12/13/2015] [Revised: 12/30/2015] [Accepted: 04/17/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND The diagnosis of irritable bowel syndrome (IBS) is challenging because of its heterogeneity and multifactorial pathophysiology. No reliable biomarkers of IBS have been identified so far. AIMS In a case-control study, using a novel application of breath analysis to distinguish IBS patients from healthy controls based on the analysis of volatile organic compounds (VOCs). Subsequently, the diagnostic VOC-biomarker set was correlated with self-reported gastrointestinal (GI) symptoms of subjects of the Maastricht IBS clinical cohort and of a general population cohort, LifeLines DEEP. METHODS Breath samples were collected from 170 IBS patients and 153 healthy controls in the clinical cohort and from 1307 participants in general population cohort. Multivariate statistics were used to identify the most discriminatory set of VOCs in the clinical cohort, and to find associations between VOCs and GI symptoms in both cohorts. RESULTS A set of 16 VOCs correctly predicted 89.4% of the IBS patients and 73.3% of the healthy controls (AUC = 0.83). The VOC-biomarker set correlated moderately with a set of GI symptoms in the clinical (r = 0.55, P = 0.0003) and general population cohorts (r = 0.54, P = 0.0004). A Kruskal-Wallis test showed no influence from possible confounding factors in distinguishing IBS patients from healthy controls. CONCLUSIONS A set of 16 breath-based biomarkers that distinguishes IBS patients from healthy controls was identified. The VOC-biomarker set correlated significantly with GI symptoms in two independent cohorts. We demonstrate the potential use of breath analysis in the diagnosis and monitoring of IBS, and a possible application of VOC analyses in a general population cohort.
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Affiliation(s)
- A Baranska
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - Z Mujagic
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Division of Gastroenterology-Hepatology, Department of Internal Medicine, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - A Smolinska
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - J W Dallinga
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
| | - D M A E Jonkers
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - E F Tigchelaar
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - J Dekens
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - A Zhernakova
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - T Ludwig
- Department of Developmental Physiology and Nutrition, Danone Nutricia Research, Utrecht, The Netherlands
| | - A A M Masclee
- Division of Gastroenterology-Hepatology, Department of Internal Medicine, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - C Wijmenga
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - F J van Schooten
- Department of Pharmacology and Toxicology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Centre (MUMC+), Maastricht, The Netherlands
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10
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Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A. Gut microbiota composition associated with stool consistency. Gut 2016; 65:540-2. [PMID: 26276682 DOI: 10.1136/gutjnl-2015-310328] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 07/23/2015] [Indexed: 12/12/2022]
Affiliation(s)
- E F Tigchelaar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - M J Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - S A Jankipersadsing
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - J Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - C Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - A Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Top Institute Food and Nutrition, Wageningen, The Netherlands
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11
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de Rooy DPC, Zhernakova A, Tsonaka R, Willemze A, Kurreeman BAS, Trynka G, van Toorn L, Toes REM, Huizinga TWJ, Houwing-Duistermaat JJ, Gregersen PK, van der Helm-van Mil AHM. A genetic variant in the region of MMP-9 is associated with serum levels and progression of joint damage in rheumatoid arthritis. Ann Rheum Dis 2014; 73:1163-9. [PMID: 23696630 DOI: 10.1136/annrheumdis-2013-203375] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVES The severity of joint destruction is highly variable between rheumatoid arthritis (RA) patients. The majority of its heritability is still unexplained. Several autoimmune diseases share genetic risk variants that may also influence disease progression. We aimed to identify genetic risk factors for the severity of joint damage in RA by studying genetic susceptibility loci of several autoimmune diseases. METHODS In phase 1, 3143 sets of x-rays of 646 Dutch RA patients taken over 7 years (Sharp van der Heijde (SHS) scored) were studied. Genotyping was done by Immunochip. Associations of single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) >0.01 and joint destruction were analysed. In phase 2, 686 North American RA patients with 926 SHS-scored x-rays over 15 years of follow-up were evaluated. In both phases multiple testing corrections were done for the number of uncorrelated SNPs; the thresholds for significance were p<1.1×10(-6) and p<0.0036. Matrix metalloproteinase 9 (MMP-9) levels were measured with ELISA in baseline serum samples. RESULTS In phase 1, 109 SNPs associated significantly with joint destruction (p<1.1×10(-6)). Of these, 76 were located in the HLA region; the 33 non-HLA variants were studied in phase 2. Here two variants were associated with the severity of joint destruction: rs451066 on chromosome 14 (p=0.002, MAF=0.20) and rs11908352 on chromosome 20 (p=0.002, MAF=0.21). Rs11908352 is located near the gene encoding MMP-9. Serum levels of MMP-9 were significantly associated with the rs11908352 genotypes (p=0.007). CONCLUSIONS These data indicate that two loci that confer risk to other autoimmune diseases also affect the severity of joint destruction in RA. Rs11908352 may influence joint destruction via MMP-9 production.
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Affiliation(s)
- D P C de Rooy
- Department of Rheumatology, Leiden University Medical Center, , Leiden, The Netherlands
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12
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Krabben A, Wilson AG, de Rooy DPC, Zhernakova A, Brouwer E, Lindqvist E, Saxne T, Stoeken G, van Nies JAB, Knevel R, Huizinga TWJ, Toes R, Gregersen PK, van der Helm-van Mil AHM. Association of genetic variants in the IL4 and IL4R genes with the severity of joint damage in rheumatoid arthritis: a study in seven cohorts. ACTA ACUST UNITED AC 2014; 65:3051-7. [PMID: 23983153 DOI: 10.1002/art.38141] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 08/13/2013] [Indexed: 11/05/2022]
Abstract
OBJECTIVE The progression of joint destruction in rheumatoid arthritis (RA) is determined by genetic factors. Changes in IL4 and IL4R genes have been associated with RA severity, but this finding has not been replicated. This study was undertaken to investigate the association between IL4- and IL4R-tagging single-nucleotide polymorphisms (SNPs) and the progression rate of joint damage in RA in a multicohort candidate gene study. METHODS IL4- and IL4R-tagging SNPs (n = 8 and 39, respectively) were genotyped in 600 RA patients for whom 2,846 sets of radiographs of the hands and feet were obtained during 7 years of followup. Subsequently, SNPs significantly associated with the progression of joint damage were genotyped and studied in relation to 3,415 radiographs of 1,953 RA patients; these included data sets from Groningen (The Netherlands), Lund (Sweden), Sheffield (UK), the North American Rheumatoid Arthritis Consortium (US), Wichita (US), and the National Data Bank (US). The relative increase in progression rate per year in the presence of a genotype was determined in each cohort. An inverse variance weighting meta-analysis was performed on the 6 data sets that together formed the replication phase. RESULTS In the discovery phase, none of the IL4 SNPs and 7 of the IL4R SNPs were significantly associated with the joint damage progression rate. In the replication phase, 2 SNPs in the IL4R gene were significantly associated with the joint damage progression rate (rs1805011 [P = 0.02] and rs1119132 [P = 0.001]). CONCLUSION Genetic variants in IL4R were identified, and their association with the progression rate of joint damage in RA was independently replicated.
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Affiliation(s)
- A Krabben
- Leiden University Medical Center, Leiden, The Netherlands
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13
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Knevel R, de Rooy DPC, Zhernakova A, Gröndal G, Krabben A, Steinsson K, Wijmenga C, Cavet G, Toes REM, Huizinga TWJ, Gregersen PK, van der Helm-van Mil AHM. Association of variants in IL2RA with progression of joint destruction in rheumatoid arthritis. ACTA ACUST UNITED AC 2013; 65:1684-93. [PMID: 23529819 DOI: 10.1002/art.37938] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Accepted: 03/12/2013] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Heritability studies have suggested an important role of genetic predisposition in the progression of joint destruction in rheumatoid arthritis (RA); the heritability is estimated at 45-58%. Several single-nucleotide polymorphisms (SNPs) have been identified as being associated with RA susceptibility. Our objective was to study the association of several of these loci with progression of joint destruction. METHODS We studied 1,750 RA patients in 4 independent data sets with 4,732 radiographs scored using the modified Sharp/van der Heijde method. Thirteen susceptibility SNPs that were not previously associated with joint destruction were tested in 596 Dutch RA patients. Subsequently, significant SNPs were studied in data sets of RA patients from North America and Iceland. Data were summarized in inverse-weighted variance meta-analyses. Further, the association with circulating protein levels was studied and the associated region was fine-mapped. RESULTS In stage 1, 3 loci (AFF3, IL2RA, and BLK) were significantly associated with the rate of joint destruction and were further analyzed in the additional data sets. In the combined meta-analyses, the minor (C) allele of IL2RA (rs2104286) was associated with less progression of joint destruction (P = 7.2 × 10(-4) ). Furthermore, the IL2RA (rs2104286) protective genotype was associated with lower (0.85-fold [95% confidence interval 0.77-0.93], P = 1.4 × 10(-3) ) circulating levels of soluble interleukin-2 receptor α (sIL-2Rα). Additionally, lower sIL-2Rα levels were associated with a lower rate of joint destruction (P = 3.4 × 10(-3) ). The association of IL2RA with the rate of joint destruction was further localized to a 40-kb region encompassing the IL2RA intron 1 and the 5' region of IL2RA and RBM17. CONCLUSION The present genetic and serologic data suggest that inherited altered genetic constitution at the IL2RA locus may predispose to a less destructive course of RA.
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Affiliation(s)
- R Knevel
- Leiden University Medical Center, Leiden, The Netherlands.
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14
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Trouw LA, Daha N, Kurreeman FAS, Böhringer S, Goulielmos GN, Westra HJ, Zhernakova A, Franke L, Stahl EA, Levarht EWN, Stoeken-Rijsbergen G, Verduijn W, Roos A, Li Y, Houwing-Duistermaat JJ, Huizinga TWJ, Toes REM. Genetic variants in the region of the C1q genes are associated with rheumatoid arthritis. Clin Exp Immunol 2013; 173:76-83. [PMID: 23607884 DOI: 10.1111/cei.12097] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2013] [Indexed: 12/15/2022] Open
Abstract
Rodent models for arthritis implicate a role for complement in disease development and progression. In humans, complement deposition has been observed in inflamed synovia of rheumatoid arthritis (RA) patients. In this study we analysed whether genetic variants of complement component C1q predispose to RA. We genotyped single nucleotide polymorphisms (SNPs) in and around the C1q genes, C1qA, C1qB and C1qC, in a Dutch set of 845 RA cases and 1046 controls. Replication was sought in a sample set from North America (868 cases/1193 controls), and a meta-analysis was performed in a combined samples set of 8000 cases and 23 262 controls of European descent. We determined C1q serum levels in relation to C1q genotypes. In the discovery phase, five of the 13 SNPs tested in the C1q genes showed a significant association with RA. Additional analysis of the genomic area around the C1q genes revealed that the strongest associating SNPs were confined to the C1q locus. Within the C1q locus we observed no additional signal independent of the strongest associating SNP, rs292001 [odds ratio (OR) = 0·72 (0·58-0·88), P = 0·0006]. The variants of this SNP were associated with different C1q serum levels in healthy controls (P = 0·006). Interestingly, this SNP was also associated significantly in genome-wide association studies (GWAS) from the North American Rheumatoid Arthritis Consortium study, confirming the association with RA [OR = 0·83 (0·69-1·00), P = 0·043]. Combined analysis, including integrated data from six GWAS studies, provides support for the genetic association. Genetic variants in C1q are correlated with C1q levels and may be a risk for the development of RA.
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Affiliation(s)
- L A Trouw
- Department of Rheumatology, Leiden University Medical Center, The Netherlands.
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15
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De Rooy D, Zhernakova A, Tsonaka R, Willemze A, Kurreeman F, Trynka G, van Toorn L, Toes R, Huizinga T, Houwing-Duistermaat J, Gregersen P, van der Helm-van Mil A. OP0049 A Genetic Variant in the Region of MMP-9 is Associated with Serum Levels and Progression of Joint Damage in Rheumatoid Arthritis. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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De Rooy D, Tsonaka R, Andersson M, Forslind K, Zhernakova A, de Kovel C, Koeleman B, van der Heijde D, Huizinga T, Toes R, Houwing-Duistermaat J, Svensson B, van der Helm-van Mil A. OP0021 Genetic Factors for the Severity of ACPA-Negative Rheumatoid Arthritis in Two Cohorts of Early Disease: A Genome-Wide Study. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Eyre S, Bowes J, Diogo D, Raychaudhuri S, Stahl E, Zhernakova A, Padyukov L, Amos C, Plenge R, Klareskog L, Gregersen P, Worthington J. OP0208 High density fine mapping in rheumatoid arthritis indentifies 14 new loci:. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2012-eular.1891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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18
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Krabben A, Wilson AG, Rooy DPCD, Zhernakova A, Brouwer E, Lindqvist E, Saxne T, Stoeken G, Nies JABV, Knevel R, Huizinga TWJ, Koeleman B, Toes R, Gregersen PK, Helm-van Mil AHMVD. A7.10 Genetic Variants in the IL-4and IL-4Receptor Genes in Association with the Severity of Joint Damage in Rheumatoid Arthritis: A Study in Seven Cohorts. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-203221.10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Knevel R, Krabben A, Wilson AG, Brouwer E, Leijsma MK, Lindqvist E, de Rooy DPC, Daha NA, van der Linden MPM, Tsonaka S, Zhernakova A, Westra HJ, Franke L, Houwing-Duistermaat JJ, Toes REM, Huizinga TWJ, Saxne T, van der Helm-van Mil AHM. A genetic variant in granzyme B is associated with progression of joint destruction in rheumatoid arthritis. ACTA ACUST UNITED AC 2013; 65:582-9. [DOI: 10.1002/art.37808] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 11/20/2012] [Indexed: 11/10/2022]
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Rooy DPCD, Zhernakova A, Tsonaka R, Willemze A, Kurreeman BAS, Toes REM, Huizinga TWJ, Houwing-Duistermaat JJ, Gregersen PK, Helm-van Mil AHMVD. A7.1 A Genetic Variant in the Region ofMMP-9is Associated with Serum Levels and Progression of Joint Damage in Rheumatoid Arthritis. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-203221.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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de Rooy DPC, Yeremenko NG, Wilson AG, Knevel R, Lindqvist E, Saxne T, Krabben A, Leijsma MK, Daha NA, Tsonaka S, Zhernakova A, Houwing-Duistermaat JJ, Huizinga TWJ, Toes REM, Baeten DLP, Brouwer E, van der Helm-van Mil AHM. Genetic studies on components of the Wnt signalling pathway and the severity of joint destruction in rheumatoid arthritis. Ann Rheum Dis 2012; 72:769-75. [PMID: 23041840 DOI: 10.1136/annrheumdis-2012-202184] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Progression of joint destruction in rheumatoid arthritis (RA) is partly heritable; knowledge of genetic factors may increase our understanding of the mechanisms underlying joint destruction. The activity of the Wnt/β-catenin pathway influences osteoblast differentiation. Dickkopf-1 (Dkk-1) and sclerostin (Sost) are negative regulators and lipoprotein receptor-related protein-5 (LRP-5) and Kremen-1 are transmembrane receptors involved in this pathway. OBJECTIVE To study variants in the genes encoding these proteins in relation to progression of joint destruction. METHODS 1418 patients with RA of four cohorts with 4885 sets of hands and feet x-rays were studied. Explorative analyses were performed on 600 patients with RA from Leiden on single nucleotide polymorphisms (SNPs) tagging Dkk-1, Sost, Kremen-1 and LRP-5. SNPs significantly associating with joint damage progression were subsequently genotyped in cohorts from Groningen (NL), Sheffield (UK) and Lund (Sweden). Data were summarised in meta-analyses. Serum levels of functional Dkk-1 and sclerostin were measured and studied in relation to genotypes. RESULTS In the first cohort, six Dkk-1, three Sost, one Kremen-1 and 10 LRP-5 SNPs were significantly associated with radiological progression of joint destruction. Three Dkk-1 SNPs were associated significantly with progression of joint damage in the meta-analysis, also after correction for multiple testing (rs1896368, rs1896367 and rs1528873). Two Sost SNPs tended to significance (rs4792909 and rs6503475, p=0.07 after false discovery rate correction). Gene-gene interactions between SNPs on Dkk-1 and Sost were seen. Serum levels of Dkk-1 were significantly correlated with the genotypes in rs1896368 (p=0.02). CONCLUSIONS Patients with RA carrying risk alleles of genetic variants in Dkk-1 have higher serum levels of functional Dkk-1 and more progressive joint destruction over time.
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Affiliation(s)
- Diederik P C de Rooy
- Department of Rheumatology, Leiden University Medical Center, PO Box 9600, Leiden 2300 RC, The Netherlands.
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Knevel R, de Rooy DP, Gregersen PK, Lindqvist E, Wilson AG, Gröndal G, Zhernakova A, van Nies JA, Toes RE, Tsonaka R, Houwing-Duistermaat JJ, Steinsson K, Huizinga TW, Saxne T, van der Helm-van Mil AH. Studying associations between variants in TRAF1-C5 and TNFAIP3-OLIG3 and the progression of joint destruction in rheumatoid arthritis in multiple cohorts. Ann Rheum Dis 2012; 71:1753-5. [PMID: 22586175 DOI: 10.1136/annrheumdis-2012-201289] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Knevel R, Krabben A, Brouwer E, Posthumus, Wilson AG, Saxne T, Lindqvist E, de Rooy DPC, Daha NA, van der Linden MPM, Stoeken-Rijsbergen G, van Toorn L, Koeleman BFC, Tsonaka S, Zhernakova A, Houwing-Duistermaat JJ, Toes REM, Huizinga TWJ, van der Helm-van Mil AHM. Genetic variants in IL-15 associate with progression of joint destruction in rheumatoid arthritis, a multi cohort study. Ann Rheum Dis 2012. [DOI: 10.1136/annrheumdis-2011-201236.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Zhernakova A, Stahl EA, Trynka G, Raychaudhuri S, Festen E, Franke L, Fehrmann RSN, Kurreeman FAS, Thomson B, Gupta N, Romanos J, McManus R, Ryan AW, Turner G, Remmers EF, Greco L, Toes R, Grandone E, Mazzilli MC, Rybak A, Cukrowska B, Li Y, de Bakker PIW, Gregersen PK, Worthington J, Siminovitch KA, Klareskog L, Huizinga TWJ, Wijmenga C, Plenge RM. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. Ann Rheum Dis 2011. [DOI: 10.1136/ard.2010.148965.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Titulaer M, Phernambucq M, Zhernakova A, van der Slik A, Wirtz P, Niks E, Martínez-Martínez P, Losen M, Bakker E, Wijmenga C, Koeleman B, De Baets M, Verschuuren J. FP59-FR-05 Genetic factors in myasthenia gravis and Lambert-Eaton myasthenic syndrome. J Neurol Sci 2009. [DOI: 10.1016/s0022-510x(09)70585-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Baas AF, Medic J, van 't Slot R, de Kovel CG, Zhernakova A, Geelkerken RH, Kranendonk SE, van Sterkenburg SM, Grobbee DE, Boll AP, Wijmenga C, Blankensteijn JD, Ruigrok YM. Association of the TGF-beta receptor genes with abdominal aortic aneurysm. Eur J Hum Genet 2009; 18:240-4. [PMID: 19672284 DOI: 10.1038/ejhg.2009.141] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is a multifactorial condition. The transforming growth factor beta (TGF-beta) pathway regulates vascular remodeling and mutations in its receptor genes, TGFBR1 and TGFBR2, cause syndromes with thoracic aortic aneurysm (TAA). The TGF-beta pathway may be involved in aneurysm development in general. We performed an association study by analyzing all the common genetic variants in TGFBR1 and TGFBR2 using tag single nucleotide polymorphisms (SNPs) in a Dutch AAA case-control population in a two-stage genotyping approach. In stage 1, analyzing 376 cases and 648 controls, three of the four TGFBR1 SNPs and nine of the 28 TGFBR2 SNPs had a P<0.07. Genotyping of these SNPs in an independent cohort of 360 cases and 376 controls in stage 2 confirmed association (P<0.05) for the same allele of one SNP in TGFBR1 and two SNPs in TGFBR2. Joint analysis of the 736 cases and 1024 controls showed statistically significant associations of these SNPs, which sustained after proper correction for multiple testing (TGFBR1 rs1626340 OR 1.32 95% CI 1.11-1.56 P=0.001 and TGFBR2 rs1036095 OR 1.32 95% CI 1.12-1.54 P=0.001 and rs4522809 OR 1.28 95% CI 1.12-1.46 P=0.0004). We conclude that genetic variations in TGFBR1 and TGFBR2 associate with AAA in the Dutch population. This suggests that AAA may develop partly by similar defects as TAA, which in the future may provide novel therapeutic options.
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Affiliation(s)
- A F Baas
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands.
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Trynka G, Zhernakova A, Romanos J, Franke L, Hunt KA, Turner G, Bruinenberg M, Heap GA, Platteel M, Ryan AW, de Kovel C, Holmes GKT, Howdle PD, Walters JRF, Sanders DS, Mulder CJJ, Mearin ML, Verbeek WHM, Trimble V, Stevens FM, Kelleher D, Barisani D, Bardella MT, McManus R, van Heel DA, Wijmenga C. Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling. Gut 2009; 58:1078-83. [PMID: 19240061 DOI: 10.1136/gut.2008.169052] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [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] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Our previous coeliac disease genome-wide association study (GWAS) implicated risk variants in the human leucocyte antigen (HLA) region and eight novel risk regions. To identify more coeliac disease loci, we selected 458 single nucleotide polymorphisms (SNPs) that showed more modest association in the GWAS for genotyping and analysis in four independent cohorts. DESIGN 458 SNPs were assayed in 1682 cases and 3258 controls from three populations (UK, Irish and Dutch). We combined the results with the original GWAS cohort (767 UK cases and 1422 controls); six SNPs showed association with p<1 x 10(-04) and were then genotyped in an independent Italian coeliac cohort (538 cases and 593 controls). RESULTS We identified two novel coeliac disease risk regions: 6q23.3 (OLIG3-TNFAIP3) and 2p16.1 (REL), both of which reached genome-wide significance in the combined analysis of all 2987 cases and 5273 controls (rs2327832 p = 1.3 x 10(-08), and rs842647 p = 5.2 x 10(-07)). We investigated the expression of these genes in the RNA isolated from biopsies and from whole blood RNA. We did not observe any changes in gene expression, nor in the correlation of genotype with gene expression. CONCLUSIONS Both TNFAIP3 (A20, at the protein level) and REL are key mediators in the nuclear factor kappa B (NF-kappaB) inflammatory signalling pathway. For the first time, a role for primary heritable variation in this important biological pathway predisposing to coeliac disease has been identified. Currently, the HLA risk factors and the 10 established non-HLA risk factors explain approximately 40% of the heritability of coeliac disease.
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Affiliation(s)
- G Trynka
- Genetics Department, University Medical Centre, University of Groningen, Groningen, The Netherlands
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Romanos J, Barisani D, Trynka G, Zhernakova A, Bardella MT, Wijmenga C. Six new coeliac disease loci replicated in an Italian population confirm association with coeliac disease. J Med Genet 2008; 46:60-3. [PMID: 18805825 DOI: 10.1136/jmg.2008.061457] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS The first genome wide association study on coeliac disease (CD) and its follow-up have identified eight new loci that contribute significantly towards CD risk. Seven of these loci contain genes controlling adaptive immune responses, including IL2/IL21 (4q27), RGS1 (1q31), IL18RAP (2q11-2q12), CCR3 (3p21), IL12A (3q25-3q26), TAGAP (6q25) and SH2B3 (12q24). METHODS We selected the nine most associated single nucleotide polymorphisms to tag the eight new loci in an Italian cohort comprising 538 CD patients and 593 healthy controls. RESULTS Common variation in IL2/IL21, RGS1, IL12A/SCHIP and SH2B3 was associated with susceptibility to CD in our Italian cohort. The LPP and TAGAP regions also showed moderate association, whereas there was no association with CCR3 and IL18RAP. CONCLUSION This is the first replication study of six of the eight new CD loci; it is also the first CD association study in a southern European cohort. Our results may imply there is a genuine population difference across Europe regarding the loci contributing to CD.
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van Vliet-Ostaptchouk JV, Shiri-Sverdlov R, Zhernakova A, Strengman E, van Haeften TW, Hofker MH, Wijmenga C. Association of variants of transcription factor 7-like 2 (TCF7L2) with susceptibility to type 2 diabetes in the Dutch Breda cohort. Diabetologia 2007; 50:59-62. [PMID: 17031610 DOI: 10.1007/s00125-006-0477-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [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] [Received: 07/04/2006] [Accepted: 09/05/2006] [Indexed: 10/24/2022]
Abstract
AIM/HYPOTHESIS A strong association between susceptibility to type 2 diabetes and common variants of transcription factor 7-like 2 (TCF7L2), encoding an enteroendocrine transcription factor involved in glucose homeostasis, has been reported in three different populations (Iceland, Denmark and USA) by Grant et al. We aimed to replicate these findings in a Dutch cohort. METHODS We analysed the genotypes of two intronic single nucleotide polymorphisms (SNPs) in TCF7L2 gene in 502 unrelated type 2 diabetes patients and in a set of healthy controls (n = 920). The two SNPs showed almost complete linkage disequilibrium (D' = 0.91). RESULTS We were able to replicate the previously reported association in our Breda cohort. The minor alleles of both variants were significantly over-represented in cases (odds ratio [OR] 1.29, 95% CI 1.09-1.52, [Formula: see text] for rs12255372; OR 1.41, 95% CI 1.19-1.66, [Formula: see text] for rs7903146). In addition, TCF7L2 haplotypes were analysed for association with the disease. The analysis of haplotypes did not reveal any strong association beyond that expected from analysing individual SNPs. The TT haplotype carrying the minor alleles was more frequent among cases (OR 1.38, [Formula: see text]). CONCLUSIONS/INTERPRETATION Our data strongly confirm that variants of the TCF7L2 gene contribute to the risk of type 2 diabetes. The population-attributable risk from this factor in the Dutch type 2 diabetes population is 10%.
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Affiliation(s)
- J V van Vliet-Ostaptchouk
- Department of Molecular Genetics, Maastricht University, Universiteitssingel 50 (UNS50/11), P.O. Box 616, 6200 MD, Maastricht, the Netherlands
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Zhernakova A, Alizadeh BZ, Eerligh P, Hanifi-Moghaddam P, Schloot NC, Diosdado B, Wijmenga C, Roep BO, Koeleman BPC. Genetic variants of RANTES are associated with serum RANTES level and protection for type 1 diabetes. Genes Immun 2006; 7:544-9. [PMID: 16855620 DOI: 10.1038/sj.gene.6364326] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RANTES (regulated on activation, normal T-cell expressed and secreted) is a T-helper type 1 (Th1) chemokine that promotes T-cell activation and proliferation. RANTES is genetically associated with asthma, sarcoidosis and multiple sclerosis. The concentration of RANTES is increased at inflammation sites in different autoimmune diseases. Type 1 diabetes (T1D) is a Th1-mediated disease with complex genetic predisposition. We tested RANTES as a candidate gene for association with T1D using three single-nucleotide polymorphism (SNP) variants (rs4251719, rs2306630 and rs2107538) to capture haplotype information. The minor alleles of all SNPs were transmitted less frequently to T1D offspring (transmission rates 37.3% (P=0.002), 38.7% (P=0.007) and 41.0% (P=0.01)) and were less frequently present in patients compared to controls (P=0.009, 0.03 and 0.04, respectively). A similar protective effect was observed for the haplotype carrying three minor alleles (transmission disequilibrium test (TDT): P=0.003; odds ratio (OR)=0.55; confidence interval (CI): 0.37-0.83; case/control: P=0.03; OR=0.74; CI: 0.55-0.98). Both patients and controls carrying the protective haplotype express significantly lower serum levels of RANTES compared to non-carriers. Subsequently, we tested a cohort of 310 celiac disease patients, but failed to detect association. RANTES SNPs are significantly associated with RANTES serum concentration and development of T1D. The rs4251719*A-rs2306630*A-rs2107538*A haplotype associated with low RANTES production confers protection from T1D. Our data imply that RANTES is associated with T1D both genetically and functionally, and contributes to diabetes-prone Th1 cytokine profile.
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Affiliation(s)
- A Zhernakova
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
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Rueda B, Zhernakova A, López-Nevot MA, Gomez-Garcia M, Ortega E, Piñero A, Correro F, Brieva JA, Nieto A, Koeleman BPC, Martín J. CTLA4/CT60 polymorphism is not relevant in susceptibility to autoimmune inflammatory intestinal disorders. Hum Immunol 2005; 66:321-5. [PMID: 15784471 DOI: 10.1016/j.humimm.2004.11.005] [Citation(s) in RCA: 19] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 11/17/2004] [Accepted: 11/22/2004] [Indexed: 12/18/2022]
Abstract
The aim of this work was to investigate the possible influence of the recently described CT60 A/G dimorphism of the CTLA4 (cytotoxic T-lymphocyte antigen 4) gene in the susceptibility to two different autoimmune inflammatory intestinal disorders, inflammatory bowel disease (IBD) and celiac disease. We analyzed a case-control cohort composed of 528 Spanish patients with IBD (284 with Crohn disease and 244 with ulcerative colitis) and 454 unrelated healthy individuals, and additionally a group of 90 celiac disease families. CT60 genotyping was performed with a TaqMan 5' allelic discrimination assay. After comparing patients with IBD with the control population, we found no significant deviation in the distribution of the alleles or genotypes of CTLA4/CT60 dimorphism. In addition, by means of familial and case-control analysis, no evidence for a statistically significant association was observed between CTLA4/CT60 and celiac disease susceptibility. Therefore, our results suggest that the CTLA4/CT60 polymorphism does not play a major role in inflammatory intestinal disorders.
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Affiliation(s)
- B Rueda
- Instituto de Parasitología y Biomedicina "López-Neyra", Granada, Spain
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Rueda B, Zhernakova A, López-Nevot MA, Martín J, Koeleman BPC. Association study of functional genetic variants of innate immunity related genes in celiac disease. BMC Med Genet 2005; 6:29. [PMID: 16078996 PMCID: PMC1190178 DOI: 10.1186/1471-2350-6-29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/29/2005] [Accepted: 08/03/2005] [Indexed: 11/10/2022]
Abstract
Background Recent evidence suggest that the innate immune system is implicated in the early events of celiac disease (CD) pathogenesis. In this work for the first time we have assessed the relevance of different proinflammatory mediators typically related to innate immunity in CD predisposition. Methods We performed a familial study in which 105 celiac families characterized by the presence of an affected child with CD were genotyped for functional polymorphisms located at regulatory regions of IL-1α, IL-1β, IL-1RN, IL-18, RANTES and MCP-1 genes. Familial data was analysed with a transmission disequilibrium test (TDT) that revealed no statistically significant differences in the transmission pattern of the different genetic markers considered. Results The TDT analysis for IL-1α, IL-1β, IL-1RN, IL-18, and MCP-1 genes genetic variants did not reveal biased transmission to the affected offspring. Only a borderline association of RANTES promoter genetic variants with CD predisposition was observed. Conclusion Our results suggest that the analysed polymorphisms of IL-1α, IL-1β, IL-1RN, IL-18, RANTES and MCP-1 genes do not seem to play a major role in CD genetic predisposition in our population.
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Affiliation(s)
- B Rueda
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC, Granada, Spain
| | - A Zhernakova
- Complex Genetics Group, Department of Biomedical Genetics, University Medical Center, Utrecht, The Netherlands
| | - MA López-Nevot
- Servicio de Inmunología, Hospital Virgen de las Nieves, Granada, Spain
| | - J Martín
- Instituto de Parasitología y Biomedicina "López-Neyra", CSIC, Granada, Spain
| | - BPC Koeleman
- Complex Genetics Group, Department of Biomedical Genetics, University Medical Center, Utrecht, The Netherlands
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Zhernakova A, Eerligh P, Wijmenga C, Barrera P, Roep BO, Koeleman BPC. Differential association of the PTPN22 coding variant with autoimmune diseases in a Dutch population. Genes Immun 2005; 6:459-61. [PMID: 15875058 DOI: 10.1038/sj.gene.6364220] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein tyrosine phosphatase PTPN22 is involved in the negative regulation of T-cell responsiveness. Recently, the association of a coding variant of the PTPN22 gene-R620W(1858C>T) with a number of autoimmune diseases has been described. Therefore, we tested the association of PTPN22 1858*T allele in Dutch early onset type 1 diabetes (T1D) and rheumatoid arthritis (RA) patients, as well as celiac disease (CD) patients, for which no previous study of PTPN22 has been reported. The PTPN22 variant was strongly associated with T1D in cases vs controls (P=2 x 10(-7), OR=2.3, 95% CI=1.7-3.1) as well as in a transmission disequilibrium test in nuclear trio's (P=9 x 10(-9), OR=3.3, CI=2.1-5.0), RA (case/control: P=0.003, OR=1.8 CI =1.2-2.6), but not CD, in spite of a trend of increased homozygosity (P=0.05) and early age at onset (P=0.01). PTPN22 is not generally associated with T-cell mediated autoimmune diseases, although it might play a role in the CD patients with early clinical manifestation.
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Affiliation(s)
- A Zhernakova
- Division of Biomedical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
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