Fig. 7: PRKG1 is expressed in RMS with a mesodermal transcriptional profile.

A Western blots showing levels and quantification of PRKG1 in primary tumors (patient samples) and xenografts (PDX). Blot representative blot of one biological replicate per patient sample. B Box plot representing PRKG1 mRNA levels on the bases of a cut-off point ( = 5.1875) (left panel). Here, we define the UpperCP (High PRKG1 levels, n = 5) versus LowerCP (Low PRKG1 levels; n = 6) samples. Mann Whitney test two-tailed Center line = median; box = 25th–75th percentiles; whiskers = min–max. ** indicates p = 0.0043. Source data are provided as Source Data file. C Hierarchical clustering of the supervised analysis of RMS primary tumors (T) and PDX (X) in UpperCP vs LowerCP samples (see Fig. 7B). D GSEA plots of the core enriched genes in high (UpperCP) versus low (LowerCP) PRKG1 samples. GSEA was performed using the Broad Institute tool with default settings. Statistical significance was assessed by permutation-based, two-sided testing with FDR adjustment. Differential expression was analyzed using limma; probes were considered significant at FDR < 0.05. E Illustration of DEGs included in Mesoderm development gene signature (GSEA: NES = 1.97, FDR = 0.00089), shown by logFC and limma p values. Source Data is available (F) Analysis of RNA-seq data from 139 RMS samples (StJude Cloud) classified into three myogenic clusters: Mesoderm/ Myoblast/ Myocyte myogenic clusters by Patel et al. (2022). PRKG1 expression levels significantly correlate with mesoderm gene signature. Gene expression (x-axis) is plotted against GSVA scores (y-axis), with a linear regression line fitted for each facet. GSVA scores, and the corresponding correlation coefficient (R) and p value are shown on each panel. The shaded area indicates the 95% confidence interval for the estimated fit. Pearson correlation test and linear regression with 95% CI (calculated as the predicted mean ± 1.96 times the standard error. G Violin plot of integrated single-nucleus RNA-seq data from all patients in Patel et al., showing PRKG1 expression across annotated clusters from the original publication. H UMAP representation of tumor cells from patient SJRHB012_R displaying annotated clusters. I UMAP representation of tumor cells from patient SJRHB012_R displaying PRKG1 expression. J UMAP representation of tumor cells from patient SJRHB012_R displaying MEOX2 expression.