Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs
Fig 2
Characterization of PAX3-FOXO1 and PAX7-FOXO1 specific transcriptomic signatures.
(a) Standardized and normalized expression levels of genes assayed by RNAseq and belonging to the 4 K-means clusters defined in S4AIII Fig and showing significant variations in their expression between control, PAX3-FOXO1 (P3F) and PAX7-FOXO1 (P7F) expressing cells. (b) Left panels: Enrichment for genes in the vicinity of cis-regulatory modules (CRMs) defined in Fig 1B (PFs CRMs, P3F CRMs, P7F CRMs are respectively clusters 1,2,3 in Fig 1B) in the gene clusters defined in (a). Right panels: Enrichment for genes associated with FP-RMS11 (FP-RMS sig.) and genes associated with PAX3-FOXO1 (P3F FP-RMS sig.) and PAX7-FOXO1 (P7F FP-RMS sig.) in RMS biopsies in the gene clusters defined in (a). Bars: -log2(p-value). (c) Heatmap of K-means clustered genes that displayed higher expression in P3F and/or P7F transfected cells compared to control cells. Fold changes across Pax3, Pax7, P3F and P7F samples are colour coded in blue (lower level) and in red (higher level). (d) Volcano plot comparing gene expression levels assayed by microarray between PAX3-FOXO1 (P3F) and PAX7-FOXO1 (P7F) biopsies, with statistical significance (-log10(p-value)) on the y-axis versus the magnitude of change (log2(fold change in PAX7-FOXO1 samples compared to PAX3-FOXO1)) on the x-axis. Grey dots: not significantly differentially expressed genes, green dots: significantly upregulated genes in PAX3-FOXO1 samples, purple dots: significantly upregulated genes in PAX7-FOXO1 samples. (e) GSEA plots showing the enrichment for genes associated to PAX3-FOXO1 activity in RMS [16] or to PAX3-FOXO1 and PAX7-FOXO1 activity in RMS (cf. d) in differentially expressed genes between control (Ctl) HFF and HFF expressing either PAX-FOXO1s (PF) or PAX3-FOXO1 (P3F) or PAX7-FOXO1 (P7F) or between P3F and P7F samples. NES: normalized enrichment score; FDR: false discovery rate.