Fig. 3: Smad4 induces different transcriptional programs in liver versus lung metastases.
a, GO analysis of upregulated genes in liver or lung metastases 7 or 14 days after Dox withdrawal. Combined scores and P values for the top KEGG (left) or Hallmark (right) pathways are shown for Smad4 on versus off for each organ and time point. Complete GO lists are provided in Supplementary Table 2. b, Heat map of representative genes from Smad4’s cytostatic or apoptotic (tumor-suppressive) and fibrogenic (tumor-promoting) transcriptional programs. The average RNA-seq log2 fold change (FC) and P values are shown for Smad4 on versus off for each organ and time point. c, Representative IF staining for Ki67 in KC-shSmad4 liver and lung metastases ± Smad4 restoration. mKate2 was used to label tumor cells. Right, quantifications (n = 12, 15, 16 and 14 independent tumors from three, four, three and three mice for the groups shown, from left to right). Analysis was performed 7 days after Dox withdrawal. d, Representative IF staining for α-SMA in KC-shSmad4 liver and lung metastases ± Smad4 restoration. mKate2 was used to label tumor cells. Right, quantifications (n = 12, 10, 12 and 11 independent tumors from three, three, three and four mice for the groups shown, from left to right). Analysis was performed at the experimental endpoint (30 days for liver; 45 days for lungs). Statistical analyses were conducted using Fisher’s exact test with Benjamini–Hochberg adjustment (a), a Wald test with negative binomial modeling and Benjamini–Hochberg adjustment (b), an unpaired two-sided t-test (c) or a two-sided Mann–Whitney U-test (d).
