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An Ileal Crohn's Disease Gene Signature Based on Whole Human Genome Expression Profiles of Disease Unaffected Ileal Mucosal Biopsies

Tianyi Zhang, Bowen Song, Wei Zhu, Xiao Xu, Qing Qing Gong, Christopher Morando, Themistocles Dassopoulos, Rodney D. Newberry, Steven R. Hunt, Ellen Li, Jacques Ravel
2012 PLoS ONE  
Previous genome-wide expression studies have highlighted distinct gene expression patterns in inflammatory bowel disease (IBD) compared to control samples, but the interpretation of these studies has been  ...  To further improve molecular classification of inflammatory bowel disease phenotypes we focused on a single anatomic site, the disease unaffected proximal ileal margin of resected ileum, and three phenotypes  ...  We also thank the faculty in the Division of Colon Rectal Surgery and the Division of Gastroenterology at Washington University for their help and support in recruiting patients.  ... 
doi:10.1371/journal.pone.0037139 pmid:22606341 pmcid:PMC3351422 fatcat:6fgthuxym5ahpaqatsftyojj2a

Intestinal receptor of SARS-CoV-2 in inflamed IBD tissue is downregulated by HNF4A in ileum and upregulated by interferon regulating factors in colon [article]

Bram Verstockt, Sare Verstockt, Saeed Adbu Rahiman, Bo-Jun Ke, Kaline Arnauts, Isabelle Cleynen, Joao Sabino, Marc Ferrante, Gianluca Matteoli, Severine Vermeire
2020 bioRxiv   pre-print
Network analyses highlighted HNF4A as key regulator of ileal ACE2, while pro-inflammatory cytokines and interferon regulating factors regulated colonic ACE2.  ...  We collected (un)inflamed mucosal biopsies from CD (n=193) and UC (n=158) patients, and 51 matched non-IBD controls for RNA sequencing, differential gene expression and co-expression analysis.  ...  Inflammatory Bowel Disease (IBD) is a prototype gastrointestinal disease characterized by a chronic relapsing inflammatory infiltrate of the small and/or large bowel.  ... 
doi:10.1101/2020.06.24.169383 fatcat:j3hw5jzwqzh2tbytyj2hdupzp4

Recent Advances in Characterizing the Gastrointestinal Microbiome in Crohn's Disease

Emily K. Wright, Michael A. Kamm, Shu Mei Teo, Michael Inouye, Josef Wagner, Carl D. Kirkwood
2015 Inflammatory Bowel Diseases  
T he pathogenesis of Crohn's disease, an inflammatory bowel disease (IBD), involves interactions between the host genome, gastrointestinal (GI) microbiota, and mucosal immune system.  ...  because of heterogeneity of study populations, differences in sample site (e.g., stool versus mucosa), and technical differences in methodology and study design.  ... 
doi:10.1097/mib.0000000000000382 pmid:25844959 pmcid:PMC4450900 fatcat:rmxscj2jxjg4dpzom7nhf7zl5u

Altered splicing associated with the pathology of inflammatory bowel disease

Kiera Berger, Hari Somineni, Jarod Prince, Subra Kugathasan, Greg Gibson
2021 Human Genomics  
Conclusions These results imply that quantitative differences in splice usage contribute to the pathology of inflammatory bowel disease in a previously unrecognized manner.  ...  To explore the possible association of aberrant splicing with inflammatory bowel disease, we developed a pipeline for quantifying transcript abundance and exon inclusion transcriptome-wide and applied  ...  The inflammatory bowel diseases (IBD), ulcerative colitis (UC), and Crohn's disease (CD) afflict approaching 1% of adults in developed countries and have been rising in prevalence globally for several  ... 
doi:10.1186/s40246-021-00347-y pmid:34301333 pmcid:PMC8305504 fatcat:t6tlx4cnazfbpjtqtj6rzw5zb4

Molecular Changes in the Non-Inflamed Terminal Ileum of Patients with Ulcerative Colitis

Ho-Su Lee, Maaike Vancamelbeke, Sare Verstockt, Tom Wilms, Bram Verstockt, João Sabino, Marc Ferrante, Séverine Vermeire, Isabelle Cleynen
2020 Cells  
Based on gene co-expression analysis, ileal changes in active ulcerative colitis patients were related to immune functions.  ...  Differential gene expression analysis with DESeq2 showed distinct expression patterns depending on disease activity and maximal disease extent.  ...  Conflicts of Interest  ... 
doi:10.3390/cells9081793 pmid:32731480 fatcat:oberawptxzhyzmxq5tifm57kzm

Importance of Bacteria as Trigger in Inflammatory Bowel Disease

Jérémy Denizot
2012 Journal of Gastrointestinal & Digestive System  
Inflammatory bowel diseases (IBD) provide a complex model of host-microbe interactions underpinning disease pathogenesis.  ...  J Gastroint Dig Syst SSN: 2161-069X JGDS, an open access journal Inflammatory Bowel Disease 20. Strober W, Fuss I, Mannon P (2007) The fundamental basis of inflammatory bowel disease.  ...  Introduction Inflammatory bowel disease (IBD) arises from complex interactions of genetic, environmental, and microbial factors [1] .  ... 
doi:10.4172/2161-069x.s8-003 fatcat:k4c3b2gizngv7n7ycgodigous4

Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn's Disease Patients

Andrew Y.F. Li Yim, Nicolette W. Duijvis, Mohammed Ghiboub, Catriona Sharp, Enrico Ferrero, Marcel M.A.M. Mannens, Geert R. D'Haens, Wouter J. de Jonge, Anje A. te Velde, Peter Henneman
2020 Journal of Clinical Medicine  
Differential methylation was predominantly found in the promoter regions of inflammatory genes.  ...  During episodes of inflammation, monocytes infiltrate the inflamed mucosa whereupon they differentiate into macrophages with a pro-inflammatory phenotype.  ...  None of the aforementioned funders had a role in the design of the study, the collection, analyses, interpretation of data, writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/jcm9041055 pmid:32276386 fatcat:r7v3cgmhurcvfea233mbusnueu

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

M. Joossens, G. Huys, M. Cnockaert, V. De Preter, K. Verbeke, P. Rutgeerts, P. Vandamme, S. Vermeire
2011 Gut  
Conclusion Unaffected relatives of patients with CD have a different composition of their microbiota compared with healthy controls.  ...  and aims A general dysbiosis of the intestinal microbiota has been established in patients with Crohn's disease (CD), but a systematic characterisation of this dysbiosis is lacking.  ...  Inflammatory bowel disease on August 22, 2011 -Published by Downloaded from Table 3 3 Median intensity of band-classes that differed significantly between unaffected  ... 
doi:10.1136/gut.2010.223263 pmid:21209126 fatcat:rhsh7zfd5valtlqkpoh5ttufua

Genetic susceptibility has a more important role in pediatric-onset Crohn's disease than in adult-onset Crohn's disease

Lissy de Ridder, Rinse K. Weersma, Gerard Dijkstra, Gerrit van der Steege, Marc A. Benninga, Ilja M. Nolte, Jan A.J. M. Taminiau, Daniël W. Hommes, Pieter C. F. Stokkers
2007 Inflammatory Bowel Diseases  
inflammatory bowel disease.  ...  Azathioprine is widely used in the treatment of inflammatory bowel disease. The occurrence of side effects, however, is a major drawback in the use of azathioprine.  ...  Het vertrouwen en de ruimte die je mij geeft in mijn ontwikkeling als MDL-arts en wetenschapper waardeer ik enorm. Prof. Dr. C.  ... 
doi:10.1002/ibd.20171 pmid:17476680 fatcat:weix5wghojhxhje3wzf27khjfm

Inflammatory bowel disease: Progress and current concepts of etiopathogenesis

2007 Journal of Digestive Diseases  
as the two main forms of inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC).  ...  Over the past few years, none of the numerous conditions that are grouped under the broad designation of 'chronic inflammatory or autoimmune disorders' has undergone as much scientific and clinical progress  ...  of genetics. 18 This is due in large part to technological advances in DNA analysis and sequencing, such as genome-wide associations (GWA), and the use of huge multicenter or multinational databases  ... 
doi:10.1111/j.1751-2980.2007.00310.x pmid:17970872 fatcat:o7ewkz2a35c37brli5cgiv6tli

Inflammatory Bowel Disease Principles and Practice

Jan Schmidt, Helmut Friess
2003 Digestive Surgery  
Overall, toxic megacolon has become a rare, but still challenging complication in IBD, especially UC.  ...  Genetic linkage analyses, through genome-wide screens, have identified a number of susceptibility loci, revealing the complexity of inflammatory bowel disease.  ...  Recently, we performed real time RT-PCR analysis on frozen mucosal samples from patients with IBD to identify genes differentially expressed in inflammatory bowel disease [4] .  ... 
doi:10.1159/000071869 fatcat:nuzjbvtwlfcplkmeaojl4x6twi

Molecular classification of Crohn's disease reveals two clinically relevant subtypes

Matthew Weiser, Jeremy M Simon, Bharati Kochar, Adelaide Tovar, Jennifer W Israel, Adam Robinson, Gregory R Gipson, Matthew S Schaner, Hans H Herfarth, R Balfour Sartor, Dermot P B McGovern, Reza Rahbar (+4 others)
2016 Gut  
Finally, expression patterns within these CD subclasses highlight large-scale differences in the immune response and aspects of cellular metabolism, and were associated with multiple clinical phenotypes  ...  Design We examined both gene expression and gene regulation (chromatin accessibility) in non-inflamed colon tissue from a cohort of adult patients with CD and control patients.  ...  ), 12 in unaffected colon mucosa from patients with CD and non-IBD.  ... 
doi:10.1136/gutjnl-2016-312518 pmid:27742763 pmcid:PMC5426990 fatcat:qudari7lmbcfbcvspdc4rdqf5i

Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis

Atle van Beelen Granlund, Arnar Flatberg, Ann E. Østvik, Ignat Drozdov, Bjørn I. Gustafsson, Mark Kidd, Vidar Beisvag, Sverre H. Torp, Helge L. Waldum, Tom Christian Martinsen, Jan Kristian Damås, Terje Espevik (+2 others)
2013 PLoS ONE  
In inflammatory bowel disease (IBD), genetic susceptibility together with environmental factors disturbs gut homeostasis producing chronic inflammation.  ...  Results: Gene expression in inflamed mucosa from UC and CD are remarkably similar. The meta-analysis confirmed this.  ...  The microarray gene expression and bioinformatics analysis was performed in collaboration with the Genomics Core Facility, Norwegian University of Science and Technology, and NMC -a national technology  ... 
doi:10.1371/journal.pone.0056818 pmid:23468882 pmcid:PMC3572080 fatcat:eoofwmntxvge5ice6yjty5b75i

Crohn's Disease-Associated Adherent-Invasive Escherichia coli Adhesion Is Enhanced by Exposure to the Ubiquitous Dietary Polysaccharide Maltodextrin

Kourtney P. Nickerson, Christine McDonald, Emiko Mizoguchi
2012 PLoS ONE  
Analysis of mucosa-associated bacteria from individuals with and without CD showed increased prevalence of malX, a gene essential for MDX metabolism, uniquely in the ileum of CD patients.  ...  Additionally, adherent-invasive E. coli (AIEC) strains are frequently isolated from ileal lesions of CD patients indicating a potential role for these strains in disease pathogenesis.  ...  The hard work of Eboni Ubinas and Tiffany Hollo of the Tissue Procurement Team and Gail West, Tammy Sadler, Eleni Stylianou and Angen Liu was essential for the collection of human samples.  ... 
doi:10.1371/journal.pone.0052132 pmid:23251695 pmcid:PMC3520894 fatcat:gpnqytydlrfgrmatmpxm7otlcm

The Genetic Predisposition and the Interplay of Host Genetics and Gut Microbiome in Crohn Disease

Hu Jianzhong
2014 Clinics in Laboratory Medicine  
Crohn's disease (CD) is a complex inflammatory bowel disease that results from a combination of genetic predispositions and environmental factors including microbiome in the digestive tract.  ...  Many of those CD susceptibility loci encode genes that play essential roles in the regulatory networks of host immune responses.  ...  The secretor status determines the expression of the ABH and Lewis histo-blood group antigens in the intestinal mucosa.  ... 
doi:10.1016/j.cll.2014.08.003 pmid:25439275 pmcid:PMC4254428 fatcat:aekwubiimnbuva4xwnsblvsd4e
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