Figure 3. BMP signaling activity in human IBD and mouse models of intestinal regeneration.

(A) Gene expression analysis of publicly available RNAseq data from human healthy and IBD tissue (GSE83687; n = 74 IBD, n = 60 control) shows downregulation of direct BMP target gene expression (ID1), variable impact on BMP ligand expression, and corresponding strong upregulation of GREM1 as the key intestinal BMP antagonist. TPM, transcripts per million. (B) ISH of BMP4, GREM1, and ID1 in healthy human colon and severe ulcerative colitis. (C) Colonic gene expression measured by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in mouse steady-state and DSS colitis shows downregulation of direct BMP target gene expression (Id1) with corresponding strong upregulation of Grem1 (n = 4 mice; P = .029 by Mann-Whitney U test). (D) ISH hybridization of Bmp4, Grem1, and Id1 in mouse steady-state and DSS colitis colon. (E) Colonic gene expression measured by qRT-PCR in mouse steady-state colon and 24 hours after 10-Gy whole-body irradiation shows minimal impact of radiation damage on BMP pathway constituent expression (n = 5 irradiated, 6 nonirradiated mice; no compared groups were significantly different). (F) ISH of Bmp4, Grem1, and Id1 in mouse steady-state colon and after 10-Gy irradiation. Scale bars: 200 μm, magnification applies to all images, except insets. Box-and-whisker plot: The horizontal line in the middle of each box indicates the median; the top and bottom borders of the box mark the 75th and 25th percentiles, respectively, the whiskers mark the standard deviation, and the circles indicate outliers. GAPDH-GOI, ratio of glyceraldehyde 3-phosphate dehydrogenase gene to the gene of interest. Statistical differences were tested using empirical Bayes moderated 2-tailed t tests with false discovery rate correction (A) or Mann-Whitney tests with false discovery rate correction (C and E). **P < .01,*** P < .001.