Fig. 3: Deregulation of an APC–RXR regulatory axis during tumor initiation establishes an OnF memory.
From: Oncofetal reprogramming drives phenotypic plasticity in WNT-dependent colorectal cancer
a, RXRa expression in matched human normal colon and tumors from TCGA/COAD (n = 41 patients). P values were calculated using two-sided, paired Wilcoxon’s test. b, Rxra expression during tumorigenesis (WT and A, n = 6 independent organoid cultures; AKSP, n = 3). The P values were calculated using two-sided, unpaired Wilcoxon’s test. In the box plots, the center line is the median, the box limits the IQR (25th to 75th percentiles) and the whiskers the highest and lowest values within ±1.5× the IQR. c, Experimental approach for the comparative analyses of Anull and RXRi (+HX531) versus WT organoids. d,e, Spearman’s correlation of the top 2,000 (d) or 1,000 (e) highly variable genes. READ, rectum adenocarcinoma. f,g, Elbow plots depicting TF activity in RXRi (f) versus WT organoids (g). TF combined binding score = −log10(P value) × log2(fold-change). Significantly more accessible or less accessible regions were used in f and g, respectively (WT, n = 2; RXR, n = 3 independent ATAC–seq experiments). h, Experimental design summary for Fig. 2i. i, GSEA of OnF genes following the APC–RXR axis perturbation during tumor initiation (n = 4 independent experiments). j,k, GSEA of OnF genes in CRC tumoroids (AKSP), following RXR-OE (j) or inhibition (RXRi) (k) (n = 4 and 3 independent experiments, respectively). l, Experimental design summary for Fig. 2m–o. m, GSEA of OnF genes >5 weeks post-RXRi washout (n = 3 independent cultures). In i–m, a two-sided permutation-based test for significance was used; P values were adjusted via the Benjamini–Hochberg method. n, ATAC–seq signal intensity in RXRi, woRXRi (>5 weeks post-HX531 withdrawal), A and AKSP versus WT organoids. o, Elbow plot of more accessible regions in RXR versus WT organoids ranked by their log2(fold-change) in woRXRi versus WT. Resolved peaks were subset to obtain the 1,342 regions (mean of number of suppressed and persistent regions) with log2(fold-change) closest to 0. The HOMER motif enrichment analysis indicates the top enriched TFBSs of the persistent ‘memory’ regions (>5 weeks post-RXRi washout (right)). n,o, RXR and woRXRi (n = 3 independent cultures; WT, A, AKSP, n = 2). FC, fold change. Illustrations in c, h and l created using BioRender.com.
