Thirty-one of the 33 patients also satisfied the Bohan and Peter criteria [14, 15]. file Rabbit Polyclonal to USP13 4: Differentially expressed genes for CD8+ T cells of PM and DM patients. Tables S8 and S9 provide differentially expressed genes for CD8+ T cells of PM and DM patients at analytical stage 1 (including potential outliers) and analytical stage 2 (excluding potential outliers), respectively. (DOCX 106 kb) 13075_2018_1688_MOESM4_ESM.docx (106K) GUID:?97DE71E0-CD9C-4C36-9B09-40D7E3D67D53 Additional file 5: Gene Ontology biological PF-04971729 processes for the differentially expressed genes in CD8+ T cells of PM and DM patients. Table S10 shows the genes mapped to the enriched GO biological processes for the differentially expressed genes in CD8+ T cells of PM and DM patients. (DOCX 17 kb) 13075_2018_1688_MOESM5_ESM.docx (18K) GUID:?D1A99FE7-A595-4EE6-931A-A17676CE1D43 Additional file 6: Differentially expressed genes in CD4+ T cells of and status, and RNA integrity number PF-04971729 [RIN]). On the contrary, in CD8+ T cells, 176 genes were differentially expressed in patients with PM compared with patients with DM. Of these, 44 genes were expressed significantly higher in CD8+ T cells from patients with PM, and 132 genes were expressed significantly higher in CD8+ T cells from patients with DM (FDR? ?0.05, model adjusted for age, sex, and RIN). Gene Ontology analysis showed that genes differentially expressed in CD8+ T cells are involved in lymphocyte migration and regulation of T-cell differentiation. Conclusions Our data strongly suggest that CD8+ T cells represent a major divergence between PM and DM patients compared with CD4+ T cells. These alterations in the gene expression in T cells from PM and DM patients PF-04971729 might advocate for distinct immune mechanisms in these subphenotypes of myositis. Electronic supplementary material The online version of this article (10.1186/s13075-018-1688-7) contains supplementary material, which is available to authorized users. [2C4]. In addition, autoantibodies are found PF-04971729 in more than 80% of the PM and DM patients, supporting a role for the adaptive immune system in the pathogenesis of these disorders [5]. In both PM and DM patients, inflammatory cell infiltrates are commonly found in the affected tissues [6, 7]. In PM, the cellular infiltrates are located mainly in the endomysium surrounding muscle fibers and typically dominated by CD8+ T cells [8, 9]. In contrast, in patients with DM, the inflammatory cell infiltrates are located mainly in the perimysium and in perivascular areas, and the infiltrates are predominated by CD4+ T cells with occasional plasmacytoid dendritic cells and B cells [6]. Further phenotyping of T cells in muscle tissue has led to the observation that the muscle-infiltrating T cells in both PM and DM are predominantly of the CD8+CD28null and CD4+CD28null phenotypes, which both have cytotoxic properties [10, 11]. Interestingly, these subpopulations of T cells can also be detected in peripheral blood of patients with myositis [10, 12]. Still, the differences in the tissue location of inflammatory cell infiltrates suggest that the underlying immune mechanisms may vary between PM and DM. In this study, we aimed to investigate whole-genome transcriptomes of CD4+ and CD8+ T cells from peripheral blood in different subsets of patients with idiopathic inflammatory myopathies (IIMs). We used RNA sequencing to identify differentially expressed genes between PM and DM, as well as in patients with both types of IIM, considering alleles. Methods Patient recruitment Initially, 33 consecutive adult PF-04971729 individuals with PM or DM (not drug-free) from the Karolinska Hospital Rheumatology Clinic were selected for the study on the basis of diagnosis (PM and DM) and status (positive and negative). Patients with myositis visited the clinic between January 21 and April 23, 2014, and were fully validated according to the new European League Against Rheumatism/American College of Rheumatology classification criteria [13]. Thirty-one of the 33 patients also satisfied the Bohan and Peter criteria [14, 15]. Extensive clinical data, including disease phenotypes and treatment regimen, were collected from clinical records by experienced rheumatologists. All patients gave written consent for their participation in the study..