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. 2020 May 1;22:39. doi: 10.1186/s13058-020-01277-8

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 5 — WT vs. S134A-GR transcriptomes in TGFβ1-treated MDA-MB-231 cells. a Principal component analysis plot derived from RNA-seq shows the differences in transcriptomes between MDA-MB-231 cells expressing either WT or S134A-GR cells and treated with vehicle or 10 ng/mL TGFβ1 for 6 h. b Volcano plot showing differential expression of genes in wt-GR+ compared to S134A-GR+ TNBC cells treated for 6 h with either Vehicle (left) or 10 ng/mL of TGFβ1 (middle). Volcano plot using the generalized linear model approach in EdgeR (comparisons of wt-GR and S134A-GR in response to TGF) to illustrate the effects of TGFβ1 treatment of cells expressing wt-GR relative to cells expressing S134A-GR (right). Red dots indicate genes with an absolute log2 fold-change of 1.0 or more and a false discovery rate of less than 0.05. Genes for GLM are detailed in Supplementary Table 1A. c Supervised heatmap shows significant differences in gene expression as measured by RNA-seq in TGFβ1-treated MDA-MB-231 cells expressing either wt-GR or S134A-GR. Rectangle indicates a cluster of interest in which genes are upregulated in response to TGFβ1 in wt-GR cells but not in the S134A-GR cells. All genes that were used for differential expression analysis are represented in this heatmap (n = 19,760). dDUSP1 and SGK1 mRNA levels were assessed using qRT-PCR following normalization to 18S expression. Mean expression of three independent replicates ± SD is shown. e Cell function and mechanism analyses of pathways via IPA of differentially expressed genes with an absolute log fold-change of 1.5 or more and a p-adjusted value of less than 0.05 in wt-GR relative to S134A-GR TNBC cells treated for 6 h with either Vehicle or TGFβ1 (10 ng/mL). f Upstream regulator analyses via IPA of differentially expressed genes with an absolute log fold-change of 1.5 or more and a p-adjusted value of less than 0.05 in wt-GR relative to S134A-GR TNBC cells treated with either Vehicle or 10 ng/mL of TGFβ1. Activation/inhibition z-scores are shown as well. Red dotted line indicates the significance value of 1.3 (p < .05)