RNA sequencing of HSkM myotubes deficient in DMD, full-length dystrophin (DP427) and utrophin reveals common transcriptomic alterations

iRNA approaches were used to knock down the expression of dystrophin (DMD), including its full-length isoform DP427, and utrophin (UTRN) genes. Specifically, iRNA-mediated knockdown of both DMD (full-length dystrophin DP427) and UTRN was performed in HSkM myotubes. It is known that the shorter dystrophin isoform DP71 compensates for full-length dystrophin DP427 in the early stages of myofiber differentiation in cell models of Duchenne muscular dystrophy. Accordingly, DP427-deficient and DP71/DP427-deficient HSkM myotubes exhibit distinct changes in the expression of genes involved in membrane integrity and cytoskeletal functions. RNA-sequencing analyses revealed overlapping transcriptomic alterations in these HSkM cell lines, which corresponded to observed phenotypic abnormalities such as increased membrane permeability and intracellular calcium levels, mitochondrial aggregation, elevated reactive oxygen species (ROS), enhanced cyto- and genotoxicity, and induction of apoptosis. Overall design: RNA-seq profiling of HSkM myotubes after siCtrl delivery and wild-type HSkM myotubes after siDMD, siDP427 and UTRN delivery. Myotubes were obtained after 12 days of differentiation.