In conclusion, our results demonstrate that miR-494-3p deficiency maintains the cross-talk between IECs (colonic crypt stem cells and differentiated IECs) and macrophages by regulating IKKβ/NF-κB-mediated recruitment of macrophages and EDA-A2/EDA2R-mediated colonic crypt stem cell survival in colitis. The gene discussed is NFKB1; the disease is colitis.