Figure 5

Significant non-muscle cell type contributions in FSHD, and their correlation with DUX4 and PAX7 signature expression. (a) Estimated relative contributions for all muscle and non-muscle cell types that show significantly different contributions in FSHD versus control muscle biopsies. See Supplemental Fig. S8 for the results of all (significant and non-significant) identified cell types. Results are based on the RNA deconvolution analysis (see “Methods” for details on PLIER analysis), based on cell types previously identified by Rubenstein AB et al.⁴⁵ (in healthy human muscle biopsies). LV: latent vector best representing the respective cell type signature noted behind the LV number. FBN1 + FAPs: Fibrilin-1 positive fibro-adipogenic progenitors. LUM + FAPs: lumican-positive fibro-adipogenic progenitors. PCV-Endothelial cells: post-capillary venules endothelial cells. (b, c) Estimated relative contribution of the Type IIa myofiber content in controls and FSHD muscle biopsies showing a reduction in Type IIa myofiber content in both DUX4^POS versus DUX4^NEG FSHD biopsies (b) and in PAX7^LOW versus PAX7^HIGH FSHD biopsies (c). (d, e) Estimated relative contribution of the LUM⁺ FAP subtype in controls and DUX4^POS versus DUX4^NEG FSHD muscle biopsies (d) and FBN1⁺ FAP subtype in controls and PAX7^LOW versus PAX7^HIGH FSHD muscle biopsies (e). p-values in (b–e) depict the results of Mann–Whitney U tests. (f–i) Linear quantitative correlation analysis for both molecular signatures [DUX4 signature (f, h) and PAX7 score (g, i)] with each FAP subtype [FBN⁺ FAPs (f, g) LUM⁺ FAPs (h, i)], showing the strongest correlation of each molecular signature with a distinct FAP subtype. For quantitative correlations, only FSHD samples were included. Grey shadings indicate the 95%-confidence interval for the linear regression line. p-values and R² values depict the result of a Pearson correlation. p-values: ns = not significant, *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. All data plots are generated in R (v4.0.3, www.R-project.org) using the packages gplots (v3.1.1), ggplot2 (v3.3.3) and ggpubr (v0.4.0). Figure and panel layout was further adapted in Adobe Illustrator CC 2018 (www.adobe.com).