Revealing predictors of disease susceptibility in dysplastic ulcerative colitis using oligonucleotide array technology

SMS Uthoff, MD, PhD,a,b NPS Crawford, MB, ChB,a W Zacharias, PhD,c MR Eichenberger, BS,a H-P Bruch, MD,b S Galandiuk, MDa

aDigestive Surgery Research Laboratory, Department of Surgery, University of Louisville School of Medicine, Louisville, KY, bSurgical Research Laboratory, Surgical Clinic, University Clinic Luebeck, Luebeck, Germany, cDepartment of Medicine and Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY

AIM: Reliable identification of dysplasia in the pre-malignant condition of ulcerative colitis (UC) is difficult due to the presence of chronic regenerative and inflammatory histology. Our goal was to determine whether genetic markers could be utilized to assess cancer risk and therefore, permit appropriate conservative treatment or surgical intervention. METHODS: Copy RNA was prepared from purified mRNA derived from human mucosal biopsies taken from dysplastic and non-dysplastic UC specimens via double-strand conversion using an oligo(dT) primer incorporating a T7 RNA polymerase binding site. Labeled targets were generated via in vitro transcription using biotinylated 11-CTP and 16-UTP. Hybridization to Affymetrix® Human Genome U95A oligonucleotide arrays was analyzed using streptavidin-phycoerythrin staining, confocal microscope scanning and the proprietary Absolute Analysis Algorithm. RESULTS AND CONCLUSIONS: mRNA profiling of dysplastic and non-dysplastic UC revealed a variety of differentially expressed genes. Interestingly, various protective modifiers of malignant transformation in UC map to susceptibility loci previously linked to inflammatory bowel disease, a spectrum of diseases that includes UC. This may appear to be antithetical, yet it may be that candidate genes of disease susceptibility neighbor those of disease immunity in the physical map of the human genome. This might explain why deciphering of the genetic basis of complex disease traits such as UC remains difficult. These results suggest that malignant transformation in UC might be governed in like genetic fashion by both susceptibility candidates and protective modifiers that map to identical loci.

KEY WORDS: Ulcerative colitis, dysplasia, candidate genes, oligonucleotide array technology.

For more information, contact

Paper presented at the International Symposium on Predictive Oncology and Intervention Strategies; Paris, France; February 9 - 12, 2002; in the section on Molecular Pathology.