GSE171724
Overactivation of wound healing-associated TGF-beta responses in EZH2-deficient decidual stromal cells.
Our objective was to identify genes upregulated by TGF-beta in control and Ezh2 cKO decidual stromal cells (DSCs), and to compare this set of genes with a previously identified gene set of H3K27me3-marked decidual genes that are putatively silenced by EZH2/PRC2 (Nancy et al. JCI. 2018). We also wanted to assess baseline (BL) gene expression in control and Ezh2 cKO DSCs, and compare it to an RNA-seq analysis of differential gene expression in whole tissue Ezh2 cKO and control decidua. RNA was isolated from untreated and TGF-beta treated decidual stromal cells from control and Ezh2 cKO mice. Sequencing provided was 706 million total reads with an average of 82.2% of these reads aligning uniquely to the mouse genome. Reads uniquely mapped to known mRNAs were used to identify gene expression changes between housing conditions using DESeq2. TGF-beta induced 638 protein-coding genes in EZH2-deficient DSCs versus 480 in control DSCs (with a 295 gene overlap), demonstrating that EZH2-deficient DSCs are transcriptionally more responsive to TGF-? (P=0.0025, Fisher's exact test). Within the 638 genes, activated fibroblast signature genes were highly over-represented. TGF-??target genes were 2.7-fold over-represented within the set of genes with higher expression in EZH2-deficient DSCs at baseline (BL; i.e., when neither EZH2-deficient nor control DSCs were treated with TGF-beta; P<1x10-20) . 741 genes were overexpressed in Ezh2 cKO DSCs compared to control DSCs, and 904 genes were underexpressed. Moreover, by comparing to our laboratory's previous CHIP-Seq analysis (Nancy et al. JCI 2018), we noted that  genes overexpressed in cKO mice were enriched in previously identified H3K27me3-marked genes (P<1x10-26). Overall design: Decidual stromal cells (DSCs) were isolated from control or Ezh2 cKO decidual tissue at E7.5 of pregnancy. Each biological isolate was split into two replicates, one of which was cultured without treatment, and one of which was cultured with 2 ng/mL of TGF-beta. Samples were cultured for 24 hours. RNA was subsequently prepared.  Next generation sequencing was performed using Illumina HiSeq 4000.