Fig. 1: Icos^-/- NOD mice developing myositis exhibit profound muscle metabolic disturbances.

a Immunofluorescence staining of immune cells (CD45) and myofibers (laminin) in the muscles of Icos^+/+ NOD and Icos^-/- NOD mice of 8, 25, and 35 weeks of age (predisease, onset and established disease in the Icos^-/- NOD mice, respectively). A representative image out of n = 10 independent mice/genotype is shown. Scale bar, 1 mm. b Cytokine (Ifng and Ifnb) and chemokine (Ccl2, Cxcl9, Cxcl10) mRNA gene expression levels in the muscles of Icos^+/+ NOD and Icos^-/- NOD mice at different ages; for Icos^+/+ NOD at all ages n = 5 independent mice/group; for Icos^-/- NOD mice, n = 8 (8 and 25 weeks of age) and n = 10 (35 weeks of age) independent mice/group (arb. units: arbitrary units). Numbers denote p values. Mean values  ±  s.e.m are shown. a, b were repeated independently twice with one representative experiment being shown. c–g Proteome analysis of Icos^-/- NOD vs. Icos^+/+ NOD mice muscles at 8, 25, and 35 weeks of age (n = 5 independent mice/genotype and age). c Number of dysregulated proteins in Icos^-/- NOD vs. Icos^+/+ NOD muscles. d Protein-protein interaction (PPI) map of dysregulated proteins in Icos^-/- NOD vs. Icos^+/+ NOD mice muscles, highlighting major altered pathways (input data corresponds to the mean of n = 5 independent mice) (STRING Gene ontology-Biological Process (GO-BP) analysis for all except for ‘Immune System’, which protein interactions were only identified by Reactome analysis). e Graphs showing the percentage of enriched STRING GO-BP and Reactome terms of the total terms for metabolic, muscle, and immune processes. f Proteins that are involved in ‘Metabolism’ (according to STRING GO-BP) were subdivided into the indicated categories based on STRING GO-BP or Reactome database analysis. g Top 15 ‘Canonical pathways’ identified using Ingenuity Pathway Analysis (IPA) of dysregulated proteins of Icos^-/- NOD vs. Icos^+/+ NOD mice. For b, statistical analyses were performed using the Two-way ANOVA test with Sidak’s post-hoc multiple comparisons. For the identification of significantly dysregulated proteins, statistical analysis was performed using the inbuilt Progenesis statistical box called ‘one-way ANOVA’. For the IPA analysis, Fisher’s Exact test was used. Source data are provided as a Source Data file.