Fig. 7. Muscle-SN induces a reparative epithelial state in organoids and rescues the reparative growth on KO iECM.

a Volcano plot showing significantly up and downregulated genes in SI organoids exposed to muscle-SN vs ENR. b GSEA of indicated gene sets comparing ENR with Muscle-SN (MSN) treated SI organoids. NES (normalized enrichment score) and FDR (false discovery rate) are depicted. c Representative maximal projection confocal images showing cytoplasmic vs nuclear YAP staining (green) in ENR vs Muscle-SN treated SI organoids. Scale 100 µm; insert is 25 µm. n = 2 independent experiments. d Representative images of WT SI organoids 3 days after splitting (scale is 650 µm), grown in the presence of indicated factors. Average area per organoid was quantified for three independent wells. e Representative immunofluorescent images of de novo crypt formation on WT and KO iECM with different treatment conditions. Matrigel-cultured 3-day old SI organoids were plated on WT and KO iECM. Adhered organoids were quantified at day 1 post-plating and de novo crypt formation per organoid was analyzed at day 7. Culture media was supplemented with either WT MSN, KO MSN, or rMMP17. Scale bar 40 µm. n = 4 samples per condition analyzed in two independent experiments. Numerical data are means ± SD and were tested by one-way ANOVA (F = 98.8; p < 0.0001) followed by Bonferoni post-test (MSN vs CHIR p < 0.001) in (d). Numerical data in (e) is average of crypts per iECM pooled from two independent experiments (n = 4 mice). One-way ANOVA (F = 3.714; p = 0.0079) and unpaired t-test to compare groups (*p < 0.05). Source data are provided as a Source Data file.