Extended Data Fig. 3: LXR activation in steady state primes the tissue for improved regeneration upon challenge.

(a) Left: representative Hematoxylin & Eosin (H&E) stained Swiss rolls and zoomed inset of distal small intestine (SI) tissue from mice fed with STD or GW3965 diet for 10 days. Right: quantification of SI crypt height and villus length. Each dot represents an individual crypt or villus (n = 4 mice). (b) Representative pictures and quantification of the number BrdU⁺ cells/crypt after 2 h pulse in the distal SI of mice fed for 10 days with STD or GW3965 diet. Each dot represents one mouse. (c) Left: representative pictures of immunofluorescence staining of SI tissue from STD or GW3965-diet fed mice after a 2 h BrdU pulse. Right: quantification of proliferating intestinal stem cells/crypt. Proliferating intestinal stem cells (ISCs) were defined as BrdU⁺Olfm4⁺ cells located underneath the uppermost wheat germ agglutinin (WGA)⁺ Paneth cells. Each dot represents one crypt and data are representative of n = 3 mice/diet group. (d) WT mice were fed with STD or GW3965-diet for 10 days and SI crypts were extracted and plated for organoid culture in ENR media in absence of additional stimuli in vitro. Representative pictures of organoids at day4 and quantification of average number of buds/organoid and % of organoids with the indicated number of buds are shown on the right. Each dot represents one mouse. The diagram was adapted from ref. ¹⁹, CC-BY 4.0. (e) Left: SI Swiss rolls shown in H&E staining and colour coded spatial transcriptomic (ST) map based on non-negative matrix factorization (NMF). Right: Quantification showing relative factor score of each of the NMF obtained from the ST map. Samples are from WT mice fed with STD or GW3965-diet for 10 days and harvested at 3dpi after 10 Gy total body irradiation (TBI). (f) Quantification of SI length from Villin-Cre:LXRα^f/fβ^f/f (LXR^ΔIEC) mice and their littermate LXRαβ^flox/flox controls. Each dot represents one mouse. (g) Representative H&E pictures and quantification of distal SI crypt and villus length from LXR^ΔIEC and littermate controls. Each dot represents one crypt or villus from n = 3 mice/group. (h) Representative pictures and quantification of the number BrdU⁺ cells/crypt after 2 h pulse from the distal SI of LXR^ΔIEC and littermate controls. Each dot represents one mouse. (i-j) Representative H&E picture and quantification of colon length from LXR^ΔIEC and littermate controls. Each dot represents one mouse. Data are representative of one (c, e, g, h and j), two (a, b, f and i) or three (d) independent experiments. Data are shown as bar plots with mean ± s.e.m. in (a-d, f-i). Significance was assessed by unpaired two-sided t test in a-c, d (buds/organoid) and f-i, two-way ANOVA with Bonferroni test in d (de novo buds) and Mann-Whitney test in e.

Source Data