ar4280-S6.DOCX (40K) GUID:?0773388A-A4EC-4089-8C22-BE45A0349F02 Additional file 7 Number S1. probes for the same gene which showed different values in expression. ar4280-S4.DOCX (37K) GUID:?56B7B044-50C5-478C-B853-82ECF1B69612 Additional file 5 Table S5. Differentially expressed genes in PBMC in JIA patients who achieved remission with methotrexate and etanercept vs. methotrexate alone. ar4280-S5.DOCX (51K) GUID:?A5961105-78DB-4604-8AC1-72495F8BAC7A Additional file 6 Table S6. Differentially expressed genes in granulocytes in JIA patients who achieved remission with methotrexate and etanercept vs. methotrexate alone. Genes listed more than once indicate different probes for the same gene which showed different values in expression. ar4280-S6.DOCX (40K) GUID:?0773388A-A4EC-4089-8C22-BE45A0349F02 Additional file 7 Physique S1. Interactions between products of differentially expressed genes in PBMC from patients HYAL1 with JIA who achieved remission using methotrexate alone (A) or Etanercept and Methotrexate (B) relative to PBMC from controls. Differentially expressed genes joined in the Ingenuity Pathway Analysis program are colored. Genes shown in red show higher expression in patients compared with controls, and those shown in green show lower expression. Genes not colored were added by the IPA program to generate these networks. ar4280-S7.PDF (678K) GUID:?02D1392D-128C-49E1-9FBF-A75987B3FC67 Additional file 8 Figure S2. Interactions between products of differentially expressed genes in granulocytes from patients with JIA who achieved remission using methotrexate alone (A) or Etanercept and Methotrexate (B) relative to granulocytes from controls. Differentially expressed genes UNC1215 joined in the Ingenuity Pathway Analysis program are colored. Genes shown in UNC1215 red show higher expression in patients compared with controls, and those shown in green show lower expression. Genes not colored were added by the IPA program to generate these networks. ar4280-S8.PDF (1.7M) GUID:?3B4F6A60-6238-4C1B-845B-025DC69E0C96 Abstract Introduction The attainment of remission has become an important end point for clinical trials in juvenile idiopathic arthritis (JIA), although we do not yet have a full understanding of what remission is at the cell and molecular level. Methods Two impartial cohorts of patients with JIA and healthy child controls were studied. RNA was prepared separately from peripheral blood mononuclear cells (PBMC) and granulocytes to UNC1215 identify differentially expressed genes using whole genome microarrays. Expression profiling results for selected genes were confirmed by quantitative, real-time polymerase chain reaction (RT-PCR). Results We found that remission in JIA induced by either methotrexate (MTX) or MTX plus a TNF inhibitor (etanercept, Et) (MTX + Et) is usually characterized by numerous differences in gene expression in peripheral blood mononuclear cells and in granulocytes compared with healthy control children; that is, remission is not a restoration of immunologic normalcy. Network analysis of the differentially expressed genes demonstrated that this steroid hormone receptor superfamily member hepatocyte nuclear factor 4 alpha (HNF4) is usually a hub in several of the gene networks that distinguished children with arthritis from controls. Confocal microscopy revealed that HNF4a is present in both T UNC1215 UNC1215 lymphocytes and granulocytes, suggesting a previously unsuspected role for this transcription factor in regulating leukocyte function and therapeutic response in JIA. Conclusions These findings provide a framework from which to understand therapeutic response in JIA and, furthermore, may be used to develop strategies to increase the frequency with which remission is usually achieved in adult forms of rheumatoid arthritis. strong class=”kwd-title” Keywords: juvenile idiopathic arthritis, methotrexate, TNF inhibitor, gene expression, biomarker, microarray Introduction The advent of biological therapies for chronic forms of arthritis has been accompanied by the hopes that: (1) therapies can be increasingly tailored to specific pathogenic pathways, decreasing unwanted side effects; and (2) by use of more targeted therapies, patients will experience more sustained periods of disease quiescence and, therefore, functional and subjective well-being. In juvenile idiopathic arthritis (JIA), the most common form of chronic arthritis in children, achieving the second of these objectives appears to be very near [1]. JIA is usually a term used to denote a heterogeneous group of childhood illnesses characterized by chronic inflammation and hypertrophy of synovial membranes. Distinct phenotypes are recognized based on disease presentation, clinical course, and specific biomarkers, for example, IgM rheumatoid factor [2]. However, even within carefully specified disease subtypes, considerable heterogeneity exists, especially with respect to response to therapy and overall outcome [3]. The biology underlying these differences is usually poorly comprehended, and obtaining a molecular understanding of phenotypic and therapeutic response differences is an important step toward developing individualized therapies for this family of diseases and their cognate conditions in adults. A major advance in pediatric rheumatology has been the recognition that treatment response can be staged based on consensus criteria developed by an international panel [4], and that these stages have biological validity that can be characterized at the molecular.