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Am J Physiol Gastrointest Liver Physiol 292: G298-G304, 2007. First published September 7, 2006; doi:10.1152/ajpgi.00321.2006
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Clinical phenotype and gene expression profile in Crohn's disease

¹Department of Gastroenterology C, Herlev Hospital; ²Department of Clinical Biochemistry, Core Unit for Microarray Analyses, Rigshospitalet; and ³Department of Medical Biochemistry and Genetics, University of Copenhagen, Copenhagen, Denmark

Submitted 19 July 2006 ; accepted in final form 1 September 2006

The clinical course varies significantly among patients with Crohn's disease (CD). This study investigated whether gene expression profiles generated by DNA microarray technology might predict disease progression. Biopsies from the descending colon were obtained colonoscopically from 40 CD patients. Gene profiling analyses were performed using a Human Genome U133 Plus 2.0 GeneChip Array, and summarization into a single expression measure for each probe set was performed using the robust multiple array procedure. Principal component analysis demonstrated that three components explain two-thirds of the total variation. The most important parameters for the determination of the colonic gene expression patterns were the presence of disease (CD) and presence of inflammation. Superimposition of clinical phenotype data revealed a grouping of the samples from patients with stenosis toward negative values on the axis of the second principal component. The functional annotation analysis suggested that the expression of genes involved in intracellular transport and cytoskeletal organization might influence the development of stenosis. In conclusion, even though most variation in the colonic gene expression patterns is due to presence or absence of CD and inflammation status, the development of stenosis is a parameter that affects colonic gene expression to some extent.

clinical presentation; inflammatory bowel disease; microarray