1 Scientific RepoRts | 7:43775 | DOI: 10.1038/srep43775 www.nature.com/scientificreports Altered gene expression and repressed markers of autophagy in skeletal muscle of insulin resistant patients with type 2 diabetes Andreas Buch Møller 1 , Ulla Kampmann 2 , Jakob Hedegaard 3 , Kasper thorsen 3 , Iver Nordentoft 3 , Mikkel Holm Vendelbo 4 , Niels Møller 2,5 & Niels Jessen 1,3,6 This case-control study was designed to investigate the gene expression profle in skeletal muscle from severely insulin resistant patients with long-standing type 2 diabetes (T2D), and to determine associated signaling pathways. Gene expression profles were examined by whole transcriptome, strand-specifc RNA-sequencing and associated signaling was determined by western blot. We identifed 117 diferentially expressed gene transcripts. Ingenuity Pathway Analysis related these diferences to abnormal muscle morphology and mitochondrial dysfunction. Despite a ~5-fold diference in plasma insulin, we did not observe any diference in phosphorylation of AKT or AS160, although other insulin-sensitive cascades, as mTOR/4EBP1, had retained their sensitivity. Autophagy- related gene (ATG14, RB1CC1/FIP200, GABARAPL1, SQSTM1/p62, and WIPI1) and protein (LC3BII, SQSTM1/p62 and ATG5) expression were decreased in skeletal muscle from the patients, and this was associated with a trend to increased phosphorylation of the insulin-sensitive regulatory transcription factor FOXO3a. These data show that gene expression is highly altered and related to mitochondrial dysfunction and abnormal morphology in skeletal muscle from severely insulin resistant patients with T2D, and that this is associated with decreased expression of autophagy-related genes and proteins. We speculate that prolonged treatment with high doses of insulin may suppress autophagy thereby generating a vicious cycle maintaining insulin resistance. Type 2 diabetes (T2D) is a complex disease that afects millions of people worldwide and the prevalence is increas- ing rapidly 1 . Te disease is characterized by impaired insulin action and accompanied hyperglycemia 2 . Exogenous insulin is commonly used to treat these patients, but some patients are extremely insulin resistant and represent a major clinical challenge in terms of achieving glycemic control despite treatment with high doses of insulin 3 . Skeletal muscle is the major organ for insulin-stimulated glucose uptake in humans 4 , and insulin resistance in skeletal muscle is a major contributor to hyperglycemia in T2D 5 . Insulin resistant skeletal muscle is characterized by abnormal morphology, including lipid accumulation and dysfunctional mitochondria 6,7 . Te molecular bases of these impairments are unknown but altered gene expression has been ascribed a critical role 8 . In accordance to this, gene expression profles from patients in the early stage of T2D include up to 100 abnormally expressed genes and many of these have structural/contractile properties or are involved in mitochondrial function and metabolism 9,10 . Whether these diferences in gene expression persist or are worsened in late stages of T2D are not known. Insulin stimulates several intracellular signaling cascades in skeletal muscle, including signaling to glucose transport, protein synthesis, and autophagy 11 . Insulin treatment to patients with T2D is primarily dosed in order to obtain glycemic control, but is ofen complicated in the late stage of T2D due to gradually increasing insu- lin requirements 12 . Impaired insulin signaling to glucose transport does not necessarily translate into similar 1 Research Laboratory for Biochemical Pathology, Department of clinical Medicine, Aarhus University, Denmark. 2 Department of internal Medicine and endocrinology, Aarhus University Hospital, Denmark. 3 Department of Molecular Medicine, Aarhus University Hospital, Denmark. 4 Department of nuclear Medicine and Pet center, Aarhus University Hospital, Denmark. 5 Medical Research Laboratory, Department of clinical Medicine, Aarhus University Hospital, Denmark. 6 Department of clinical Pharmacology, Aarhus University Hospital, Denmark. correspondence and requests for materials should be addressed to n.J. (email: niels.jessen@clin.au.dk) Received: 17 October 2016 Accepted: 30 January 2017 Published: 02 March 2017 OPEN