Large-Scale Integrative Analysis of Epigenetic Modifications Induced by Isotretinoin, Doxycycline and Metronidazole in Murine Colonic Intestinal Epithelial Cells

Environmental factors are playing a central role in triggering inflammatory responses in the intestine. There is increasing evidence that the development of inflammatory bowel disease (IBD) is deriving from an aberrant immune response to the commensal gut microbiota triggered by various environmental factors in a susceptible host. A vitamin A derivate used in acne therapy (isotretinoin) has been inconsistently associated with the onset of IBD. However, what needs to be considered is the previous treatment of acne patients with antibiotics that are also associated with the development of IBD, thus representing a crucial confounding factor. Here, we studied whether doxycycline (acne therapy), metronidazole (IBD therapy) or isotretinoin are able to induce alterations in DNA methylation and microRNA expression patterns in murine colonic intestinal epithelial cells (IECs). Additionally, we analyzed time-dependent changes in the aforementioned epigenetic mechanisms to study how epigenetic signatures evolve over time. As for changes in DNA methylation, we found isotretinoin to have strong demethylating effects, while antibiotic treatment had only a moderate impact. Isotretinoin-mediated demethylation resolved after a washout phase, not supporting an association between isotretinoin treatment and IBD. Regarding microRNA and mRNA expression, isotretinoin and doxycycline, but not metronidazole, potentially induce long-term changes in microRNA/mRNA expression profiles towards the down-regulation of immune responses. Analysis of time-dependent DNA methylation showed stable marks over a time frame of 4 weeks. Furthermore, novel microRNAs were identified (e.g., microRNA-877-3p), which might be of relevance in IEC development.