Fig. 3. Transcriptomic analysis of quadriceps muscles from male WT and Actn3 KO mice injected with saline or dexamethasone after 3 or 24 hours.

(A) Heatmap of robustly regulated genes highlights the magnitude of response to dexamethasone treatment after 3 hours. Volcano plots of the effects of dexamethasone treatment (B) and Actn3 KO (C) demonstrate the efficacy of both interventions and the scale of transcriptional responses. Vertical dashed lines represent a log₂ fold change (FC) of −1 or 1, and horizontal dashed lines represent a value of q = 0.05. (D) Correlation plots show that both Actn3 KO and WT mice exhibit broadly similar transcriptional responses to dexamethasone at 3 and 24 hours after injection. Genes with observed q < 0.15 for an interaction test between the treatment, time after injection, and genotype factors are highlighted in orange. (E) The log₂-normalized expression of a selection of these genes highlights the difference in dexamethasone response between WT and Actn3 KO (means ± SEM). Symbols represent individual mice. (F) Gene set enrichment analysis describes a broadly immunosuppressive characterization of the dexamethasone response and known skeletal muscle phenotypes of Actn3 KO; gene sets showed the down-regulation in the dexamethasone-treated and Actn3 KO animals, respectively. (G) Barcode plots suggest greater down-regulation within GO_POSITIVE_REGULATION_OF_LYMPHOCYTE_ MIGRATION, the top ranked gene set for the interaction effect, in WT but not Actn3 KO. Enrichment is a relative measure compared to a uniform distribution of t statistics within the gene set, represented by the dashed horizontal line. (For each genotype, n = 3 for saline and n = 5 for dexamethasone-treated groups)