GSE123141
Intestinal macrophage mRNA sequencing of patients with colonic inflammatory bowel disease and a cohort of healthy controls
The objective of this study was to investigate the role of intestinal macrophages in inflammatory bowel disease.  A prospective observational study was completed. Gut biopsies from patients with Ulcerative Colitis, Crohn's Disease and Healthy donors were harvested.  Using Fluorescence-activated cell sorting a purified CD14+/CD163+ intestinal macrophage population was isolated. RNA extracted and amplified from this population of macrophages was subjected to RNA-sequencing and bioinformatically analysed. The most relevant candidates were validated with RT-qPCR and immunohistochemistry. Intestinal macrophages in UC and CD patients show a strong reprograming with over 1200 and 800 dysregulated genes, respectively. UC and CD intestinal macrophages showed an activated M1 inflammation associated to the attraction and activation of inflammatory T-cells and a Th1 immune response. Interestingly, macrophages from CD also showed a significant activation of M2 genes, associated with a Th2 response. Mirroring clinical observations, CD (but not UC) macrophages showed enrichment of expression of fibrotic and granuloma genes. Both UC and CD macrophages are down-regulating genes engaged in drug/xenobiotics metabolism roles key for IBD therapy (such as TPMT). Key genes such as MMP12 (fibrosis), CXCL9 (T-cell attraction) and CD40 (T-cell activation) were confirmed by RT-qPCR and also at the protein level by immunohistochemistry. Overall design: This study evaluated mRNA expression in 28 human macrophage samples from three disease groups: ulcerative colitis, Crohn's disease, and healthy controls.