title: Whole genome gene expression meta-analysis of inflammatory bowel disease colon mucosa demonstrates lack of major differences between Crohn's disease and ulcerative colitis.
abstract: BACKGROUND
  In inflammatory bowel disease (IBD), genetic susceptibility together with environmental factors disturbs gut homeostasis producing chronic inflammation. The two main IBD subtypes are Ulcerative colitis (UC) and Crohn's disease (CD). We present the to-date largest microarray gene expression study on IBD encompassing both inflamed and un-inflamed colonic tissue. A meta-analysis including all available, comparable data was used to explore important aspects of IBD inflammation, thereby validating consistent gene expression patterns.
  
  
  METHODS
  Colon pinch biopsies from IBD patients were analysed using Illumina whole genome gene expression technology. Differential expression (DE) was identified using LIMMA linear model in the R statistical computing environment. Results were enriched for gene ontology (GO) categories. Sets of genes encoding antimicrobial proteins (AMP) and proteins involved in T helper (Th) cell differentiation were used in the interpretation of the results. All available data sets were analysed using the same methods, and results were compared on a global and focused level as t-scores.
  
  
  RESULTS
  Gene expression in inflamed mucosa from UC and CD are remarkably similar. The meta-analysis confirmed this. The patterns of AMP and Th cell-related gene expression were also very similar, except for IL23A which was consistently higher expressed in UC than in CD. Un-inflamed tissue from patients demonstrated minimal differences from healthy controls.
  
  
  CONCLUSIONS
  There is no difference in the Th subgroup involvement between UC and CD. Th1/Th17 related expression, with little Th2 differentiation, dominated both diseases. The different IL23A expression between UC and CD suggests an IBD subtype specific role. AMPs, previously little studied, are strongly overexpressed in IBD. The presented meta-analysis provides a sound background for further research on IBD pathobiology.
authors.affiliation: Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway.
authors.forename: Atle van Beelen
authors.initials: Av
authors.lastname: Granlund
authors.forename: Arnar
authors.initials: A
authors.lastname: Flatberg
authors.forename: Ann E
authors.initials: AE
authors.lastname: Østvik
authors.forename: Ignat
authors.initials: I
authors.lastname: Drozdov
authors.forename: Bjørn I
authors.initials: BI
authors.lastname: Gustafsson
authors.forename: Mark
authors.initials: M
authors.lastname: Kidd
authors.forename: Vidar
authors.initials: V
authors.lastname: Beisvag
authors.forename: Sverre H
authors.initials: SH
authors.lastname: Torp
authors.forename: Helge L
authors.initials: HL
authors.lastname: Waldum
authors.forename: Tom Christian
authors.initials: TC
authors.lastname: Martinsen
authors.forename: Jan Kristian
authors.initials: JK
authors.lastname: Damås
authors.forename: Terje
authors.initials: T
authors.lastname: Espevik
authors.forename: Arne K
authors.initials: AK
authors.lastname: Sandvik
mesh_terms: D000328:Adult; D000368:Aged; D023181:Antimicrobial Cationic Peptides / Q000235:genetics; D016000:Cluster Analysis; D003093:Colitis, Ulcerative / Q000235:genetics / Q000276:immunology; D003106:Colon / Q000276:immunology / Q000378:metabolism*; D003424:Crohn Disease / Q000235:genetics / Q000276:immunology; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics* / Q000276:immunology; D007413:Intestinal Mucosa / Q000276:immunology / Q000378:metabolism*; D008297:Male; D008875:Middle Aged; D006377:T-Lymphocytes, Helper-Inducer / Q000276:immunology / Q000378:metabolism; D055815:Young Adult
chemical_list: D023181:Antimicrobial Cationic Peptides