BRB-seq data of murine intestinal organoids treated with 100ng/ml of Egf, Ereg or Nrg1 ligand for 24 h

Regeneration of the intestinal epithelium is a dynamic process requiring a transient Yap-dependent reprogramming of the epithelium into a fetal-like state. Adjacent stroma, including subepithelial fibroblasts, are believed to coordinate the process, but mechanisms are not well understood. Here, we identify Neuregulin 1 (NRG1) and Epiregulin (EREG) as fibroblast-derived EGF ligands in colon and intestine which are induced during regeneration and capable of supporting the growth of the intestinal epithelium. While EREG stimulated intestinal organoid growth similarly to EGF, NRG1 increased de novo crypt formation. The goal of this experiment was to observe the differences in gene expression profile of stromal-derived EGF ligands EREG and NRG1 on intestinal organoids compared to traditional used EGF. Organoids were derived from intestinal crypts of a WT mice C57BL/6J. To exclude the size differences observed in long term cultures of EREG and NRG1, we first cultured the organoids for three days in normal ENR media, removed exogenous EGF for 24h and added EGF, EREG or NRG1 to the culture medium for 24 hours prior to the RNA isolation. NRG1 treated organoids acquired a fetal/regenerative transcriptome including activation of the Yap pathway and induction of epithelial EGF ligand Ereg and Amphiregulin (Areg) expression, highlighting the dynamic orchestration of the EGF signaling during regeneration. Overall design: Total of 18 samples from two experiments. The intestinal crypts were isolated from two different WT mice for organoid culture. Intestinal crypts were treated first 3 days in ENR, then 24h without any EGF ligand and 24h with either EGF,EREG or NRG1. Three replicates for each ligand.