To assess the changes in the immune cell landscape of the human small intestine (hSI) in CeD we separated the epithelium from LP (see methods) and isolated CD45+ immune cells separately from LP and the epithelial layer of duodenal biopsies obtained from newly diagnosed CeD patients (n = 8), patients who are on gluten-free diet (GFD) for at least one year (n = 5) and from control individuals without CeD (Ctrl) (n = 7). Here, PTPRC is linked to cranioectodermal dysplasia.