Epigenetics of Crohn’s Disease, Ulcerative Colitis, and Phenotypically Normal Individuals

Abstract

Background It is difficult to distinguish between Crohn’s disease and ulcerative colitis, as they share many symptoms and many susceptibility genetic loci. Due to the similarities in phenotype between Crohn’s disease and ulcerative colitis, many patients are misdiagnosed for years. For this project, I collected genetic material, medical histories, and environmental variables from individuals with Crohn’s disease, individuals with ulcerative colitis, and individuals that are phenotypically normal. The purpose of this project is to determine the differential epigenetic methylation of genes in individuals with Crohn’s disease and ulcerative colitis compared to phenotypically normal controls. Materials and Methods Participants were recruited for this project at the Kansas Medical Center. Twenty of these individuals had Crohn’s disease, ten had ulcerative colitis, and thirty-one were phenotypically normal. Buccal swabs and information relevant to this project (via a questionnaire) was collected from the individuals. DNA was extracted then bisulfite-converted so that the unmethylated cytosines would be converted to uracils. Real-time PCR was performed on the promoter regions of three genes both prior to and post-bisulfite conversion, as well as on the regions of the genes containing known associated SNPs. The three genes of interest in this project are the NOD2, ATG16L1, and PTPN2 genes. Each of these genes has been found to be associated with Crohn’s disease. These three genes work in concert by identifying pathogenic bacteria, forming a response, and ultimately clearing out the bacteria. Results The statistical tests used in this project showed a few significant differences between Crohn’s disease, ulcerative colitis, and phenotypically normal samples from the questionnaire. From the bisulfite-converted samples, however, there were no obvious differences between the three groups.