Relevance of mouse and human IBD patient-derived colon organoids to investigate intestinal macrophage differentiation

The gastrointestinal tract is a remarkable example of complex biology, with a constant dialogue between the intestinal epithelium, in close contact with the microbiota, and the immune cells that protect the gut from infection. Organoids have revolutionized our approach to modeling the intestinal cellular compartment and have opened new avenues for unraveling the mechanisms involved in intestinal homeostasis and chronic pathogenesis, such as inflammatory bowel disease. To date, few models have been established to explore the role of the colon, which is, however, the main site of inflammation in ulcerative colitis. Here, we used conditioned media produced by colon organoids from mice or humans (control patients and patients with ulcerative colitis) to investigate the relationship between macrophages and the colon epithelium. We addressed transcriptomic profiles of organoid conditioned media-stimulated bone marrow-derived macrophages and found that these cells exhibited a unique anti-inflammatory signature distinct from that of conventional in vitro IL-4/IL-13 M2-differentiated macrophages. In addition, organoid conditioned media induced a clear CD5 antigen-like-mediated immunoregulatory effect characterized by a significant reduction in lipopolysaccharide-induced inducible nitric oxide synthase expression. In line, organoid conditioned media from human colons inhibited lipopolysaccharide-dependent inflammatory cytokine expression in human monocyte-derived macrophages. Interestingly, the inflammatory marker CD68 was reduced by organoid conditioned media from control patients but not from patients with ulcerative colitis, suggesting epithelial dysfunction in patients with ulcerative colitis. Our results report new regulatory mechanisms in the colon and highlight the importance of developing new in vitro models to better characterize the relationship between the intestinal epithelium and immune mucosal cells.