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. Author manuscript; available in PMC: 2023 Apr 14.
Published in final edited form as: Clin Cancer Res. 2022 Oct 14;28(20):4466–4478. doi: 10.1158/1078-0432.CCR-22-0384

Figure 6. Transcriptional antagonism between HOXD13 and EWS::FLI1 is evident at single-cell resolution.

Figure 6.

A-B) Venn diagrams of the overlap between HOXD13 bound (CUT&RUN) and regulated (RNAseq) genes in each cell line. C-D) Heatmaps show the relative change in expression of these “direct” targets with shHOXD13. E) Overrepresentation analysis of EWS::FLI1 repressed gene sets identified as enriched among directly HOXD13-activated target genes. Data were generated using CITE-seq. F) Scatter plot of HOXD13 expression and the IC-EwS EWS::FLI1 signature by cell line. G) Scatter plot of HOXD13 expression and the IC-EwS EWS::FLI1 signature by PDX. H) Scatter plot of HOXD13 expression and the IC-EwS EWS::FLI1 signature by primary tumor sample. Scatter plot of HOXD13 activated genes and EWS::FLI1 repressed genes colored by the mesenchyme development (GO:0060485) gene set score in I) Ewing cell lines, J) PDX lines, and K) primary tumor samples. J) Summary model of HOXD13 cooperation and antagonism with EWS::FLI1 (Biorender). r: Pearson’s correlation coefficient.