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

<div><h3>Background</h3><p>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.</p> <h3>Methods</h3><p>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.</p> <h3>Results</h3><p>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 <em>IL23A</em> which was consistently higher expressed in UC than in CD. Un-inflamed tissue from patients demonstrated minimal differences from healthy controls.</p> <h3>Conclusions</h3><p>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 <em>IL23A</em> 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.</p> </div

Initial analysis of NTNU data set.

<p>A: PCA analysis of NTNU data set. Each point represents one sample, with colour indicating sample groups as described in figure legend. Axis indicate % of total variance explained in each component. B: Venn diagram illustrating the relationship between analyses of sample groups UC and CD directly and using N as common reference. Numbers indicate significant genes (corrected p-val<0.05).</p

Antimicrobial peptide gene expression.

<p>The figure shows a heat map of t-scores (corrected p-val <0.05) for genes coding for known antimicrobial peptides. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056818#pone.0056818.s005" target="_blank">Figure S5</a> shows the same data with no p-value cut-off. Each column in the figure represents the result for one comparison against normal control, with the sample source and test group given as column name. The connection between each column’s source abbreviation and its related dataset(s) and article(s) are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056818#pone-0056818-t002" target="_blank">table 2</a>. Some sets lack measurements for certain genes, in which case a grey marking is used.</p

T helper cell associated GSEA analysis.

<p>A subset of gene categories thought to represent T helper cell differentiation was selected from MSigDB. The bar plot is a summary of results from GSEA analysis of this subset, where each bar represents the mean GSEA score for a sample group (UC or CD) for the GSEA category in question. A Wilcox rank-sum test was performed between disease groups fails to identify a difference between GSEA scores for the selected categories.</p

Summary of sample information.

<p>Each column summarizes characteristics for all patients contributing with samples to the corresponding sample groups. 5-ASA – 5-aminosalicylic acid. S-ASA – sulphasalazine. Sample groups are abbreviated N for normal controls, CD for Crohn’s disease, UC for ulcerative colitis, CDU for un-inflamed Crohn’s disease and UCU for un-inflamed ulcerative colitis.</p

Meta-analysis data source.

<p>Information on all data sets used in meta-analysis. Column “Name” refers to abbreviations used in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056818#pone-0056818-g002" target="_blank">Figure 2</a>- and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056818#pone.0056818.s001" target="_blank">Figure S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056818#pone.0056818.s005" target="_blank">S5</a>. “Study title” refers to name of original source article, with reference given in column “PMID [Ref]”. Column “No. samples” gives number of samples in each group in the relevant data set, with the following group names: N – Normal controls, CD – Crohn’s disease, UC – Ulcerative colitis, CDU – Un-inflamed Crohn’s disease and UCU – Un-inflamed ulcerative colitis. Column “Platform” refers to microarray technology used in the relevant analysis.</p