Fig. 5: GRIP1 is required for the establishment of M2IL4 and M2GC transcriptomes.
a, b Expression of (a) GRIP1 or (b) IL4- (top) GC- (middle) or shared (bottom) M2 target genes in WT and GRIP1 cKO M0, M2IL4, M2Cort, and M2Dex populations as assessed by RT-qPCR. The average relative expression of each transcript in WT M0 is arbitrarily set to 1. n = 4 biological replicates [mice]; One-tailed unpaired t test; p-values are indicated; ns, non-significant (p ≥ 0.05). Error bars are SEM. c Stacked bar plot shows the number of DEGs (FC ≥ 1.5) in GRIP1 cKO as a fraction of WT M2IL4, M2Dex, or shared DEGs relative to M0 (RNAseq, WT: n = 3, cKO: n = 4 biological replicates). d GRIP1 peaks from Fig. 4b were annotated to their closest gene using ChIPseeker, and overlap with GRIP1-independent (n = 1516) or -dependent (n = 432) DEGs from (c) was determined for all unique peaks. A bar graph shows the % (and number) of genes in each subset associated with IL4- and/or Dex-induced peaks. The P-value for overrepresentation was determined by bootstrapping samples from the whole GRIP1 peak atlas to determine how often a set of N peaks would contain the observed overlap with each gene list by chance. e Volcano plot shows DEGs in GRIP1 cKO vs. WT in M2IL4 (left) and M2Dex (right) relative to M0 of each genotype. (FC ≥ 1.5, unadjusted p-value < 0.05). Selected inflammation-related genes expressed at higher levels in the cKO M2IL4 and M2Dex relative to WT are highlighted in red. Key M2 target genes downregulated in the cKO are highlighted in both M2IL4 (orange) and M2Dex (green). Examples of the shared M2IL4:M2Dex GRIP1 target genes are underlined. f Differentially regulated pathways (unadjusted p < 0.01 defined as in Fig. 1d) identified using QuSAGE with MsigDB canonical pathways subset (Broad Institute) are shown for GRIP1 cKO vs. WT in M2IL4 (left) and M2Dex (right). Select pathways are labeled (upregulated, red; downregulated, orange for IL4 and green for Dex); M2IL4:M2Dex-shared pathways are underlined. Circle size is proportional to the number of genes in the pathway, and color signifies the p-value. Source data are provided as a Source data file.
