Defining the host mucosal and gut microflora interactions in Crohn's disease using redundancy analysis on microarray datasets

Introduction: Crohn’s disease (CD) is an inflammatory bowel disease that is characterised by chronic relapsing inflammation of the digestive tract. There is a significant body of evidence that suggests the intestinal mucosal microbiome interacts with the immune response to produce pathological inflammation and together these factors play a major role in the pathogenesis of CD. The aim of this study is to investigate interactions between the human intestinal mucosal transcriptome and mucosal microbiome using multivariate redundancy analysis on microarray datasets. Methods: DNA and RNA were extracted from the same mucosal biopsies collected from CD patients (terminal ileum: n=5 from sites with active disease, n=4 from inactive sites (tissue with normal histology); colon: n=8 from active and n=6 from inactive sites). RNA was used to study the human intestinal mucosal transcriptome (Affymetrix GeneChip® Exon 1.0 ST arrays) and DNA was used to study the resident microbiota using a custom phylogenetic microarray. The latter was designed using published gastrointestinal microbiota 16S rRNA sequences with ~ 40-mer oligonucleotides targeting 765 bacterial species. Through examining the expression arrays, 30 differentially expressed inflammatory response genes of interest were selected. Correlations between expression patterns for these genes were assessed. Representatives (TNFRSF1B, IL2RA, IL8) of three groups of inflammatory genes with highly correlated expression and three uncorrelated genes of interest (CXCL11, IL- 13RA1 and TIRAP) were used. Multivariate relationships between the expression of the six representative inflammatory response genes and the abundance of microbial species in colon or terminal ileum, in patients with active or inactive disease was examined using redundancy analysis using the vegan package in R1. Correlations between the expression of individual inflammatory response genes and the abundance of individual microbes were also investigated. Results