Fig. 3

Proteomic analysis of DMD and CAPN3 knock downs in 3D-tissue-engineered-skeletal muscle. A Effect of knock down on Calpain-3 (CAPN3) and dystrophin protein levels as a function of time in 3D-TESMs. For reference, the abundances of vinculin and GAPDH are shown. Data are expressed as log2 LFQ values and represented as means ± SD derived from three independent 3D-TESMs at each timepoint. B Volcano plot of the CAPN3 knock down compared to the non-targeting control at day 7. Proteins that were significantly up and downregulated are indicated in red and blue, respectively. Average protein LFQ values were derived from three independent 3D-TESMs from each timepoint. Proteins were considered significant when FDR was < 0.05 in ≥ 2 timepoints. C Supervised clustering of the CAPN3 knock down. Clusters with similar expression changes over time are indicated. Clustering was based on the Z-scores of the LFQ values of significant proteins in the CAPN3 knock down relative to the non-targeting control. n = total number of proteins per cluster. D Z-scores of each protein cluster from C. E Top 5 enriched GO pathways in the upregulated protein clusters of the CAPN3 knock down. F Top 5 enriched GO pathways in the downregulated protein clusters of the CAPN3 knock down. G Heatmap of proteins found significantly altered in the CAPN3 knock down relative to the non-targeting control. Colors and numerical values represent the mean LFQ as a percentage of the most enriched condition. H–M as B–G but for the knock down of DMD