IBD transcriptome

Inflammatory bowel diseases (IBD) are a group of chronic inflammatory conditions of the gastrointestinal tract that are associated with multiple pathogenic factors, including dysregulation of the immune response. Effector CD4 T cells and regulatory CD4 T cells (Treg) are central players in maintaining the balance between tolerance and inflammation. Interestingly, genetic modifications in these cells have been implicated in regulating the commitment of specific phenotypes and immune functions. However, the transcriptional program controlling the pathogenic behavior of T helper cells in IBD progression is still unknown. In this study, we aimed to find master transcription regulators controlling the pathogenic behavior of effector CD4 T cells upon gut inflammation. To achieve this goal, we used an animal model of IBD induced by the transfer of naive CD4 T cells into recombination-activating gene 1 (Rag1) deficient mice, which are devoid of lymphocytes. As a control, a group of Rag1 mice received the transfer of the whole CD4 T cells population, which includes both effector T cells and Treg. When gut inflammation progressed, we isolated CD4 T cells from the colonic lamina propria and spleen tissue, and performed bulk RNA-seq.